clades.nextstrain.org Open in urlscan Pro
2600:9000:224a:c400:10:acd5:b680:93a1  Public Scan

Form analysis
0 forms found in the DOM

Text Content

Nextclade
 * Citation
 * Docs
 * Settings
 * What's new
 * English
   EnglishالعربيةDeutschEspañolFrançaisItaliano한국어PortuguêsРусский中文
 * 
 * 
 * 

To Results


NEXTCLADE

v1.14.0

Clade assignment, mutation calling, and sequence quality checks

SELECT A PATHOGEN



 * SARS-COV-2
   
   Reference: Wuhan-Hu-1/2019 (genbank: MN908947)
   
   Updated: 2022-04-08 12:00 (UTC)

 * INFLUENZA A H1N1PDM HA
   
   Reference: A/California/07/2009 (genbank: CY121680)
   
   Updated: 2022-01-18 12:00 (UTC)

 * INFLUENZA A H3N2 HA
   
   Reference: A/Wisconsin/67/2005 (genbank: CY163680)
   
   Updated: 2022-01-18 12:00 (UTC)

 * INFLUENZA B VICTORIA HA
   
   Reference: B/Brisbane/60/2008 (genbank: KX058884)
   
   Updated: 2022-01-18 12:00 (UTC)

 * INFLUENZA B YAMAGATA HA
   
   Reference: B/Wisconsin/01/2010 (genbank: JN993010)
   
   Updated: 2022-01-18 12:00 (UTC)

 * SARS-COV-2 WITHOUT RECOMBINANTS
   
   Reference: Wuhan-Hu-1/2019 (genbank: MN908947)
   
   Updated: 2022-04-08 12:00 (UTC)

Recent dataset updates
Next


FOR MORE ADVANCED USE-CASES:

NEXTCLADE CLI

Nextclade CLI is a command line version of this web application.

It is a single-file, standalone executable, consumes the same inputs and the
same outputs as this web application, but is faster, more configurable and more
convenient for scripting, automation, and integration into bioinformatics
pipelines. Nextclade CLI is available for as a single-file download for
different platforms and as a Docker container image. After download, type
"nextclade --help" to get started.

 * Linux
 * macOS (Intel)
 * macOS (Apple Silicon)
 * All versions
 * nextstrain/nextclade
 * Documentation

NEXTALIGN CLI

Nextalign CLI is a sequence reference alignment tool.

It uses the same alignment algorithm as Nextclade. Useful if you only need
sequence alignment and translated peptides, without full analysis and quality
control features. It is available as a set of static executables for different
platforms and as a Docker container image. After download, type "nextalign
--help" to get started.

 * Linux
 * macOS (Intel)
 * macOS (Apple Silicon)
 * All versions
 * nextstrain/nextalign
 * Documentation

NEXTSTRAIN

Nextclade is part of Nextstrain.

Nextstrain is an open-source project to harness the scientific and public health
potential of pathogen genome data. It provides continually-updated view of
publicly available data with powerful analyses and visualizations showing
pathogen evolution and epidemic spread. The goal is to aid epidemiological
understanding and improve outbreak response.

Learn more about Nextstrain project as a whole, and about its subprojects.

 * nextstrain.org
 * Source code
 * Documentation: Home
 * Documentation: Augur
 * Documentation: Auspice
 * Documentation: Nextstrain CLI
 * auspice.us


WHAT IS NEXTCLADE?

Nextclade is a tool that identifies differences between your sequences and a
reference sequence used by Nextstrain, uses these differences to assign your
sequences to clades, and reports potential sequence quality issues in your data.
You can use the tool to analyze sequences before you upload them to a database,
or if you want to assign Nextstrain clades to a set of sequences.

To analyze your data, drag a fasta file onto the upload box or paste sequences
into the text box. These sequences will then be analyzed in your browser -- data
never leave your computer. Since your computer is doing the work rather than a
server, it is advisable to analyze at most a few hundred sequences at a time.
Nextclade currently only supports SARS-CoV-2, but we will hopefully extend the
tool to other pathogens on Nextstrain.

The source code for the application and algorithms is opensource and is
available on GitHub. User manual is available at
docs.nextstrain.org/projects/nextclade.


WHAT ARE THE CLADES?

Nextclade was originally developed during COVID-19 pandemic, historically
primarily focused on SARS-CoV-2, and at the time of writing, this is still the
main use-case. This section describes clades with application to SARS-CoV-2, but
Nextclade can analyse other pathogens too.

19A19B20A20B20C20E21A (Delta)21B (Kappa)21D (Eta)21H (Mu)20D20F20I (Alpha)20J
(Gamma)21E (Theta)21M (Omicron)20G20H (Beta)21C (Epsilon)21F (Iota)21I
(Delta)21J (Delta)21G (Lambda)21K (Omicron)21L (Omicron)Fig.1. Illustration of
phylogenetic relationships of SARS-CoV-2 clades, as defined by Nextstrain

Since its emergence in late 2019, SARS-CoV-2 has diversified into several
different co-circulating variants. To facilitate discussion of these variants,
we have grouped them into clades which are defined by specific signature
mutations.

We currently define 18 major clades (see this blog post for details):

 * 19A and 19B emerged in Wuhan and have been dominating the early outbreak
 * 20A emerged from 19A out of dominated the European outbreak in March and has
   since spread globally
 * 20B and 20C are large genetically distinct subclades 20A emerged in early
   2020
 * 20D to 20I have emerged over the summer of 2020 and include three "Variants
   of Concern" (VoC).
 * 21A to 21F include the VoC delta and several Variants of Interest (VoI).

Within Nextstrain, we define each clade by its combination of signature
mutations. You can find the exact clade definition in
github.com/nextstrain/ncov/defaults/clades.tsv. When available, we will include
WHO labels for VoCs and VoIs.

Learn more about how Nextclade assigns clades in the documentation.


NEXTCLADE IS A PART OF NEXTSTRAIN PROJECT. NEXTCLADE IS MAINTAINED BY:


CORNELIUS ROEMER

Staff ScientistNeherLab, Biozentrum, University of BaselSwiss Institute of
Bioinformatics
 * 
 * 


IVAN AKSAMENTOV

Senior Software EngineerNeherLab, Biozentrum, University of BaselSwiss Institute
of Bioinformatics
 * 


RICHARD NEHER

Principal InvestigatorNeherLab, Biozentrum, University of BaselSwiss Institute
of Bioinformatics
 * 
 * 
 * 


WE ARE THANKFUL TO OUR CONTRIBUTORS:


CHRISTOPHER BOTTOMS


EMMA HODCROFT


THOMAS SIBLEY


ALEX RUBINSTEYN


FINLAY MAGUIRE


DNANTO


NATALIE STROUD


VICTOR LIN


THEO SANDERSON

Nextclade (c) 2020-2022 Nextstrain developers

version 1.14.0 (commit: d45cd63, build: 1440, branch: release)


WHAT'S NEW

×


NEXTCLADE WEB 1.14.0, NEXTCLADE CLI 1.11.0, NEXTALIGN CLI 1.11.0 (2022-03-15)


[FEATURE] NEXTCLADE PANGO CLASSIFIER (SARS-COV-2 SPECIFIC)

With the latest dataset, Nextclade now assigns sequences a pango lineage,
similar to how clades are assigned. The classifier is about 98% accurate for
sequences from the past 12 months. Older lineages are deprioritised, and
accuracy is thus worse. Read more about the method and validation against
pangoLEARN and UShER in this report: Nextclade as pango lineage classifier:
Methods and Validation.


[FEATURE] BETTER TREE EXTENSIONS #741

The Nextclade extensions fields in reference tree JSON now contain more
information. This makes custom clade-like columns on the results page more
informative.


[FEATURE] UPDATE AUSPICE

The tree rendering component, Auspice, was updated to version 2.34.1. Refer to
its changelog for details.


[FIX] MUTATION BADGES SHOWING INCORRECT POSITION FOR FIRST NUCLEOTIDE #745

We fixed a bug where mutations at position 1 were incorrectly showing position 0
in Nextclade Web


NEXTCLADE WEB 1.13.2, NEXTCLADE CLI 1.10.3, NEXTALIGN CLI 1.10.3 (2022-02-15)

This is a bug fix release.


[FIX] IGNORE PRIVATE REVERSIONS OF DELETIONS WHEN CALCULATING DIVERGENCE

Since their introduction, individual private reversions of deletions contributed
extra to divergence. This was unexpected, so we removed reversions of deletions
from consideration when calculating divergence in Nextclade.


[FIX] SORT PRIVATE SUBSTITUTIONS ON THE TREE

Private substitutions are now sorted by position when they are displayed on the
tree page


[FIX] "TRUNCATED" TEXT IN THE INSERTIONS TOOLTIP

In Nextclade Web, long insertions no longer have a visual bug when the
"truncated" text is displayed twice.


NEXTCLADE WEB 1.13.1, NEXTCLADE CLI 1.10.2, NEXTALIGN CLI 1.10.2 (2022-02-01)

This is a bug fix release.


[FIX] EXCLUDE REVERSIONS OF DELETIONS FROM CONSIDERATION IN "SNP CLUSTERS" QC
RULE

Since introduction of reversions in Nextclade Web 1.13.0 and Nextclade CLI
1.10.0, "SNP clusters" QC rule have been including reversions of deletions when
counting clustered private mutations. This was unexpected and produced
false-positives for some of the sequences. To fix that, we removed the
reversions of deletions from consideration of this QC rule, so that it behaves
as previously.


[FIX] CENTER MARKERS IN SEQUENCE VIEW IN NEXTCLADE WEB

In this version we improved the display of various colored markers (mutations,
ranges etc.) in sequence and peptide views on the Results page of Nextclade Web.
The individual markers are now centered around their position in the sequence
(previously left-aligned). Although markers have moved by just a few pixels,
this makes positioning more consistent, and ensures that different types of
markers are correctly aligned across table rows.


NEXTCLADE CLI 1.10.1 (2022-01-26)


[FIX] IMPROVE ERROR MESSAGE WHEN THE VIRUS PROPERTIES FILE IS MISSING #704

Since version 1.10.0 Nextclade CLI have introduced a new required input file,
virus_properties.json and datasets and documentation were updated to match.
However, users who don't use datasets might have encountered breakage due to a
missing file: when running Nextclade CLI without either --input-dataset of
--input-virus-properties flag provided, it would stop with an unclear error
message. In this release we improve the error message, making sure that that
explains the problem and offers a solution.

This does not affect Nextclade Web or Nextalign CLI.

In order to facilitate upgrades, for most users, we recommend to:

 * download the latest dataset before each Nextclade CLI session (e.g. in the
   beginning of an automated workflow, or once you start a batch of experiments
   manually) using nextclade dataset get command
 * use --input-dataset flag instead of individual --input-* flags for dataset
   files when issuing nextclade run command
 * if necessary, override some of the individual input files using corresponding
   --input-* flags


[FIX] ADD INFORMATION ABOUT VIRUS_PROPERTIES.JSON OR --INPUT-VIRUS-PROPERTIES TO
CHANGELOG

In the excitement of bringing the new features, we forgot to mention
virus_properties.json or --input-virus-properties in the changelog when
Nextclade CLI 1.10.0 was released. We now added this information retroactively.


NEXTCLADE WEB 1.13.0, NEXTCLADE CLI 1.10.0, NEXTALIGN CLI 1.10.0 (2022-01-24)


💥 [BREAKING CHANGE] NEXTCLADE: NEW REQUIRED INPUT FILE: VIRUS_PROPERTIES.JSON
#689

This version introduces a new required input file for Nextclade, called
virus_properties.json. This file contains additional information necessary for
the "Detailed split of private mutations" feature (see below). The new versions
of Nextclade datasets were released to account for this change.

How it affects different tools in the Nextclade family and how to upgrade:

 * Nextclade Web - requires the new file. Migration path: no action is needed.
   Nextclade Web always uses the latest dataset automatically.

 * Nextclade CLI - requires the new file. Migration path:
   
   * Download the latest dataset with nextclade dataset get command (dataset
     tagged 2022-01-18T12:00:00Z or more recent is required)
   * If using --input-dataset flag: the new file will be be picked up
     automatically from the latest dataset. No further action is needed.
   * If not using --input-dataset flag: add --input-virus-properties flag to
     pint to virus_properties.json file from the dataset.

 * Nextalign CLI - not affected: it does not use virus_properties.json.
   Migration path: no action is needed.


[FEATURE] DETAILED SPLIT OF PRIVATE MUTATIONS (NEXTCLADE) #689

Private mutations (differences between a query sequence and nearest neighbour in
reference tree) are now split into three categories:

 1. Reversion to reference genotype
 2. (SARS-CoV-2 only for now) Mutation to a genotype common in at least 1 clade
    get labeled with that clade
 3. Mutations that are neither reversions nor labeled (called "unlabeled")

Which category a mutation belongs to is visible by hovering over the "Mut."
column in Nextclade Web and in various "privateNucMutations" fields in
csv/tsv/json outputs.


[CHANGE] "PRIVATE MUTATIONS" QC RULE NOW ACCOUNTS FOR REVERSIONS AND LABELED
MUTATIONS

Reversions and labeled mutations (see feature above) are particularly common in
contaminated samples, coinfections and recombination. To draw the user's
attention to such sequences, both types of private mutation now get higher
weights in the "Private mutations" QC rule (denoted as "P" in Nextclade Web, and
qc.privateMutations in output files).


[FEATURE] INSERTIONS NOW ALSO AVAILABLE AS AMINO ACIDS #692

Aminoacid insertions in the query peptides relative to the corresponding
reference peptide are now displayed in the "Ins." column in Nextclade Web and
are emitted as "aaInsertions" and "totalAminoacidInsertions" fields in Nextalign
and Nextclade output files. Note, that similarly to nucleotide insertions,
aminoacid insertions are stripped from the output alignment.


[FIX] GAPS IN QUERY SEQUENCES ARE NOW STRIPPED CORRECTLY #696

When query sequences contained gaps (-), e.g. when inputting aligned sequences,
gaps were not stripped correctly since v1.7.0 (web v1.10.0), which could lead to
- showing up in insertions.


NEXTCLADE WEB 1.12.0, NEXTCLADE CLI 1.9.0, NEXTALIGN CLI 1.9.0 (2022-01-11)


[FEATURE] HANDLE "-" STRAND GENE TRANSLATION

The strand column in the gene map file was previously ignored. Now the "-"
strand genes are correctly reverse-complemented before translation.


[FEATURE] UPDATE SARS-COV-2 CLADE SCHEMA

The schema that illustrates the tree of SARS-CoV-2 clade on the main page of
Nextclade Web was updated to account for recent clade changes.


[FIX] CENTER MUTATION MARKERS IN SEQUENCE VIEWS

Previously the mutation markers in sequence views in results table of Nextclade
Web were anchored to their position in the sequence view on their left edge.
They are now correctly centered around their position, such that the center of
marker is at the corresponding position in the sequence.


[FIX] CORRECT EXIT CODES

Nextclade CLI and Nextalign CLI could sometime exit with incorrect exit code.
This has been fixed.


[FIX] CORRECTLY HANDLE EMPTY PEPTIDES

The alignment algorithm in Nextclade CLI and Nextalign CLI could sometimes
produce translation that is longer than expected, when the translated sequence
is empty. Now the empty peptides are discarded and a warning is issued.


[FIX] ENSURE ARRAY BOUNDARIES

In rare cases Nextclade and Nextalign algorithms could sometimes read past the
end of arrays, which previously went undetected. This is now fixed.


NEXTCLADE WEB 1.11.1, NEXTCLADE CLI 1.8.1 (2022-01-07)


[HOTFIX] NEXTCLADE CLI CRASHES ON MACOS WHEN READING JSON TREE (#680)

Fixes crash Error: [json.exception.invalid_iterator.214] cannot get value | when
reading JSON tree on macOS


NEXTCLADE WEB 1.11.0, NEXTCLADE CLI 1.8.0 (2022-01-04)


[FEATURE] BETTER DATASET SELECTOR

Nextclade Web has got the new dataset selector on the main page, which clearly
presents all available dataset and is more convenient to use. The last selected
dataset is remembered, so that it dow not need to be selected again on
subsequent runs. This also fixes rare problems and inconsistencies, when
incorrect dataset might have been used despite another dataset is being
selected.


[FEATURE] DYNAMIC NODE ATTRIBUTES

Nextclade CLI and Nextclade Web now can assign multiple clade-like attributes to
the analyzed sequences.

If input reference tree JSON contains an array of attribute keys attached to the

meta.extensions.nextclade.clade_node_attrs_keys = ["my_clades", "other_clades"]


For each query sequence, during clade assignment step, Nextclade will lookup
values of these keys from .node.node_attrs property of the nearest reference
tree node and assign them to the corresponding properties of the newly attached
nodes, just like it happens with the usual Nextstrain clades. This feature is
currently not used with the default datasets, but we are planning to extend the
reference trees in these datasets to take advantage of this feature. Curious
users can start experimenting with their own reference trees and custom
nomenclatures. Learn more about clade assignment in Nextclade in the
documentation.


[PERFORMANCE] OPTIMIZE MATCH TABLE LOOKUPS

In this version, alignment algorithm behind Nextclade and Nextalign is now up to
10% faster due to performance improvements in nucleotide and aminoacid table
lookups.


NEXTCLADE WEB 1.10.0, NEXTCLADE CLI 1.7.0 (2021-12-09)


[PERFORMANCE] OPTIMIZE FASTA PARSER

The new optimized FASTA parser makes Nextclade CLI up to 60% faster and
Nextalign CLI up to 500% faster when used on high-core-count machines. Nextalign
and Nextclade now scale much better with number of available threads and rely
less on I/O speed. See #632 for more details.


[FIX] AVOID CRASH DUE TO BUFFER OVERFLOW

This is an internal fix of a problem that might have lead to a crash in rare
cases, when coordinate map array was accessed beyond it's size.


NEXTCLADE WEB 1.9.0, NEXTCLADE CLI 1.6.0 (2021-12-07)


[BREAKING CHANGE][FIX] REMOVE UNUSED CLI FLAGS FOR AMINOACID SEED ALIGNMENT

Seed matching step was removed in Nextalign and Nextclade CLI 1.5.0, however the
command-line parameters previously providing configuration options for this step
were not. In this version, the now unused family of --aa-* CLI flags is removed.
Migration path: remove these flags from Nextclade CLI invocation.


[FEATURE] MAKE "RESULTS" AND "TREE" PAGES FULL-WIDTH IN NEXTCLADE WEB

The content in "results" and "tree" pages of Nextclade Web now occupies entire
width available in the browser window, so that more useful information can be
presented. In particular, sequence views should be more readable, especially on
larger screens.


[FEATURE] DYNAMICALLY ADJUST WIDTH OF AA MUTATION MARKERS

Nextclade Web now dynamically adjusts width of AA mutation markers in sequence
views to avoid overly long mutation groups that may obscure other mutations.
This is particularly important for sequences with high density of mutations.


[FEATURE] REDUCE PROBABILITY OF WEBWORKER TIMEOUT ERRORS

On low-end computers, computers with slow internet connection or computers under
heavy background resource utilization Nextclade Web could sometimes produce
WebWorker timeout errors. This has been addressed by increasing the timeout
interval from 10 seconds to 1 minute.

If this is not enough, consider freeing up system memory and CPU resources by
closing unused applications and browser tabs, processing sequences in smaller
batches, or using Nextclade CLI.


[FIX] FIX OFF-BY-ONE ERRORS IN INSERTION POSITIONS

Nextclade Web, Nextclade CLI and Nextalign could sometime produce incorrect
positions for nucleotide insertions - off by 1 nucleotide to either direction.
This was fixed in the new version.


[FIX] DON'T ADD PRIVATE REVERSIONS WHEN QUERY AMINOACID IS UNKNOWN

In previous versions, if a query sequence, for one reason or another, had
aminoacid X at the position where the parent tree node had a private mutation,
Nextclade was incorrectly calling a new reversion at this position. This is now
fixed and Nextclade will not report a reversion. We assume that in these
situations the sequencing defect is more likely than a reversion.


[FIX] AVOID POTENTIAL DEREFERENCE OF NULLOPT

This is an internal fix of a problem that might have lead to a crash, but never
manifested so far.


[FIX] AVOID ERROR WHEN --GENES FLAG CONTAINS A SUBSET OF GENES

Nextclade 1.8.0 introduced an error when --genes flag contained only a subset of
genes from the gene map. This is now resolved.


NEXTCLADE WEB 1.8.1, NEXTCLADE CLI 1.5.1 (2021-11-27)


[FIX] AVOID CRASH WHEN RELATIVE SHIFT (BANDWIDTH) IS LARGER THAN QUERY LENGTH

In rare cases Nextclade 1.5.0 could crash during alignment of some of the short
peptides. This has been fixed in this version.


[FIX] IMPROVE PEPTIDE ALIGNMENT

We improved heuristics which determine band width and shift for the peptide
alignment, so that some of the peptides with large insertions can now be
aligned.


NEXTCLADE WEB 1.8.0, NEXTCLADE CLI 1.5.0 (2021-11-27)


[FEATURE] IMPROVE PEPTIDE ALIGNMENT

We improved the algorithm for peptide alignment. Instead of performing seed
matching in order to estimate width of the band and shift parameters for peptide
alignment, we now deduce these parameters from the nucleotide alignment results.
This allows Nextclade to align and analyse some of the peptides that would fail
previously, including for low quality gene sequences and sequences with large
deletions or deletions close to the beginning.


[FIX] ACCOUNT FOR THE PARTIALLY COVERED LAST CODON IN FRAME SHIFT

Nextclade previously did not account for the last codon in a frame shift if that
codon was covered by the shift only partially. In this version we count the
partial codons. This solves an issue with empty frame shift codon ranges being
reported in rare cases. This change may result in some of the frame shifts to be
longer by 1 codon in the new version compared to previous versions of Nextclade.
The nucleotide length of frame shifts stays the same.

None of the ignored frame shift ranges in the QC configurations of the existing
dataset are affected by this change. But if you use a custom QC configuration,
some of the frame shifts in the list of ignored frame shifts might need to be
adjusted.


[FIX] FIX CRASHES WITH NEXTCLADE CLI ON MACOS

In this version we fixed a crash with segmentation fault that could sometimes
happen with Nextclade CLI on macOS.


NEXTCLADE WEB 1.7.4 (2021-11-16)

This is a bugfix release for Nextclade Web.


[FIX] ENSURE THAT URL PARAMETERS ALWAYS HAVE EFFECT

Due to an internal error in Nextclade Web, sometimes inputs provided using URL
parameters were ignored. This has been fixed now. Only users and external
integrations which explicitly use URL parameters to pass data into Nextclade Web
were affected. See documentation for Nextclade Web: URL parameters for more
details.


[FEATURE] UPDATE AUSPICE

In this release we updated Nextstrain Auspice (the tree visualization package)
to version v2.32.1, with the new features and bug fixes. See Auspice project's
changelog for more details.


NEXTCLADE WEB 1.7.3, NEXTCLADE CLI 1.4.5 (2021-11-04)

This is a bugfix release for Nextclade Web and Nextclade CLI.

After Nextclade Web version 1.7.3 and Nextclade CLI version 1.4.3 the "Private
mutations" QC check was incorrectly counting individual deletions, rather than
contiguous ranges of deletions, as it was before that. This resulted in QC score
being too high for sequences that have many deletions. In this version we ensure
again that the deletion ranges are counted. This should now bring the "Private
mutations" QC score back to what is expected.


NEXTCLADE CLI 1.4.4 (2021-11-01)

This is a bugfix release for Nextclade CLI.


[FIX] PREVENT NEXTCLADE CLI FAILING WITH ERROR "LIBRARY NOT LOADED"

The mistake in the Nextclade CLI build was fixed and now it should not look for
external libraries on macOS.


NEXTCLADE WEB 1.7.2, NEXTCLADE CLI 1.4.3 (2021-11-01)

This is a bugfix release for nextclade Web and Nextclade CLI.


[FIX] PROPERLY DISPLAY PRIVATE AMINOACID MUTATIONS ON THE TREE

This release ensures that both nucleotide and aminoacid mutations on the
branches of the phylogenetic tree leading to the nodes representing analyzed
sequences are properly displayed and that the corresponding information is
correctly written to the output tree JSON. Similarly to how it's done in the
main Nextstrain project, these mutations are private, i.e. called relative to
the parent node.

The internal reorganization of the code responsible for finding private
mutations might also make Nextclade slightly faster and to consume less memory.


NEXTCLADE CLI 1.4.2 (2021-10-26)

This is a small bugfix release and only affects Nextclade CLI. Nextclade Web and
Nextalign CLI are unchanged.


[FIX] CRASH IN DATASET LIST COMMAND ON MACOS

Nextclade CLI could sometimes crash on macOS when issued a dataset list command
due to an internal error. This was now fixed.


[FIX] UNINFORMATIVE ERROR MESSAGE WHEN QC CONFIG IS MISSING

When both --input-dataset and --input-qc-config flags are omitted Nextclade CLI
now produces a more informative error message, as was intended. Thanks Peter
Menzel (@pmenzel) for the report.


NEXTCLADE WEB 1.7.1, NEXTCLADE CLI 1.4.1 (2021-10-05)


[FIX] FORMAT OF CSV/TSV OUTPUT FILES

We fixed a few mistakes in CSV and TSV output files, such as missing last
delimiter when the "errors" column is empty, inconsistent application of
quotation marks and incorrect numeric formats - decimals when integers should
be.


NEXTCLADE WEB 1.7.0, NEXTCLADE CLI 1.4.0, NEXTALIGN CLI 1.4.0 (2021-09-30)


[FEATURE] FRAME SHIFT DETECTION

Nextclade now can detect reading frame shifts in the analyzed sequences and
report them in the web interface as well as in the output files.

BACKGROUND

Frame shift occurs when a sequence contains a range of indels (deletions and/or
insertions) and the total length of this range is not divisible by 3. In this
case the grouping of nucleotides into codons changes compared to the reference
genome and the translation of this region manifests in the peptide as a range
consisting almost entirely from aminoacid mutations.

Frame shifts can often be found towards the end of genes, spanning until or
beyond the gene end. Sometimes, when indels occur in multiple places, the ones
that follow can compensate (cancel) the frame shift caused by the previous ones,
resulting in frame shift that spans a range in the middle of the gene. In these
cases, due to extreme changes in the corresponding protein, the virus is often
not viable, and are often a sign of sequencing errors, however, cases of
biological frame shifts are also known. Sometimes, frame shifts can also
introduce premature stop codons, causing the gene to be truncated. The premature
stop codons within frame shifts are currently not (yet) detected by Nextclade.

PREVIOUS BEHAVIOR

Previously, Nextclade was not able to detect frame shifts ranges specifically.
Instead, a frame shift was suspected in a gene when the gene length was not
divisible by 3 (hinting to indels of a total length not divisible by 3). In
these cases the entire gene was omitted from translation, a warning was issued,
and aminoacid changes in that gene could not be detected and reported.

NEW BEHAVIOR

Now that Nextclade knows the exact shifted ranges for each gene, it translates
the genes with frame shifts, but masks shifted regions with aminoacid X (unknown
aminoacid). The aminoacid changes in non-frame-shifted regions within such genes
are now reported. This means that in some sequences Nextclade can now detect
more mutations than previously. The affected genes are now emitted into the
output fasta files instead of being discarded.

FRAME SHIFTS REPORT IN NEXTCLADE WEB

Frame shifted ranges are denoted as red horizontal (strikethrough) lines with
yellow highlights in the "Sequence view" and "Gene view" columns of the results
table of Nextclade Web. The new "FS" column shows number of detected frame
shifts: unexpected and known (ignored) ones (see the QC changes below for more
details).

FRAME SHIFTS REPORT IN THE OUTPUT FILES

Frame shifted ranges (in codon coordinates) are reported in CSV and TSV output
files in column named frameShifts and in JSON output file under frameShifts
property.


[FEATURE] IMPROVED FRAME SHIFT QUALITY CONTROL (QC) RULE

Previously, frame shift quality control rule (denoted as "F" in Nextclade Web)
was relying on gene length to reason about the presence of frame shifts - if a
gene had length not divisible by 3 - a warning was reported.

Now this rule uses the detected frame shift ranges to make the decision. There
now can be more than one frame shift detection per gene and Nextclade now
accounts for compensated frame shifts, which were previously undetected.

In the new implementation of the Frame Shift QC rule, some of the frame shift
ranges are considered "ignored" or "known" (as defined in qc.json file of the
dataset). These frame shifts don't cause QC score penalty.


[FEATURE] NEW VERSION OF SARS-COV-2 DATASET

We simultaneously release a new version of SARS-CoV-2 dataset, which contains an
updated tree and clades, as well as a new set of frame shift ranges and stop
codons to ignore. For the details refer to the dataset changelog.

Nextclade Web uses the latest version of the datasets by default and CLI users
are encouraged to update their SARS-CoV-2 dataset with the nextclade dataset get
command.


[FEATURE] OPTIONAL TRANSLATION BEYOND FIRST STOP CODON

By default Nextalign CLI and Nextclade CLI translate the whole genes, even if
stop codons appear during translation. In this release we added a flag
--no-translate-past-stop, which if present, makes translation to stop on first
encountered stop codon. The remainder of the peptide is the filled with gap (-)
character. This might be useful in some cases when a more biological behavior of
translation is desired.


NEXTCLADE WEB 1.6.0, NEXTCLADE CLI 1.3.0, NEXTALIGN CLI 1.3.0 (2021-08-31)


[FEATURE] NEXTCLADE DATASETS

In this release we introduce Nextclade Datasets, a convenient way of downloading
files required for Nextclade analysis. Now data files (such as reference
sequences, reference tree and others) are served for all users from a central
dataset repository.

DATASETS IN NEXTCLADE WEB

The dropdown menu in Nextclade Web now allows user to chose between available
datasets before analysis and automatically fetches the latest files from the
central dataset repository.

DATASETS IN NEXTCLADE CLI

Nextclade CLI gained new commands and flags to manage datasets:

 * nextclade dataset list command allows to list available datasets
 * nextclade dataset get command allows to download a dataset to a directory
 * nextclade run command runs the analysis (for compatibility with old version
   the word run can be omitted) and the new --input-dataset flag allows to
   specify the directory of the previously downloaded dataset

QUICK EXAMPLE

nextclade dataset get --name=sars-cov-2 --output-dir=data/sars-cov-2

nextclade run \
  --input-fasta=data/sars-cov-2/sequences.fasta \
  --input-dataset=data/sars-cov-2 \
  --output-tsv=output/nextclade.tsv \
  --output-tree=output/nextclade.auspice.json \
  --output-dir=output/


See Nextclade CLI documentation for example usage and Nextclade Datasets
documentation for more details about datasets.

Note, data updates and additions are now decoupled from Nextclade releases. The
datasets will be updated independently. Read datasets documentation on dataset
versioning and a trade-off between reproducibility or results vs latest features
(e.g. clades and QC checks).


[FEATURE] FLU DATASETS IN NEXTCLADE

With this release, additionally to the previously available SARS-CoV-2 dataset,
we introduce 4 new Influenza datasets:

 * Influenza A H1N1pdm (rooted at "A/California/07/2009")
 * Influenza A H3N2 (rooted at "A/Wisconsin/67/2005")
 * Influenza B Victoria (rooted at "B/Brisbane/60/2008")
 * Influenza B Yamagata (rooted at "B/Wisconsin/01/2010")

These datasets allow Nextclade to analyze sequences for these pathogens.

Nextclade Datasets feature simplifies adding new pathogens in Nextclade and we
hope to add new datasets in the future.


[DEPRECATION] DATA FILES IN NEXTCLADE GITHUB REPOSITORY ARE DEPRECATED

The files in /data directory of the Nextclade GitHub repository are now
deprecated in favor of Nextclade Datasets feature.

These files will be deleted from repository on October 31st 2021, but will be
still available in git history. We do not recommend to use these files, as they
will no longer be updated.


NEXTCLADE WEB 1.5.4 (2021-08-16)

[FEATURE] ADD "DOCS" LINK

Top navigation bar now contain an new link "Docs", which points to Nextclade
Documentation site (https://docs.nextstrain.org/projects/nextclade).


NEXTCLADE CLI 1.2.3, NEXTALIGN CLI 1.2.3 (2021-08-12)

This release only affects docker images. There are no actual changes in
Nextclade CLI, Nextalign CLI or Nextclade Web. They should behave the same as
their previous versions.

[CHANGE] ADD CA-CERTIFICATES PACKAGE INTO DEBIAN DOCKER IMAGES

For better compatibility with workflows, this adds CA certificates into the
Debian docker images. They are necessary for SSL/TLS to be working, in
particular when fetching data.

These are the default images when you pull nextstrain/nextclade and
nextstrain/nextalign without specifying a tag or specifying one of the debian
tags. Issue docker pull nextstrain/nextclade to refresh the local image to the
latest version.


NEXTCLADE CLI 1.2.2, NEXTALIGN CLI 1.2.2 (2021-08-12)

This release only affects docker images. There are no actual changes in
Nextclade CLI, Nextalign CLI or Nextclade Web. They should behave the same as
their previous versions.

[CHANGE] ADD PS UTILITY INTO DEBIAN DOCKER IMAGES

This adds ps utility into the Debian docker images. For better compatibility
with nextflow workflows.

These are the default images when you pull nextstrain/nextclade and
nextstrain/nextalign without specifying a tag or specifying one of the debian
tags.


NEXTCLADE WEB 1.5.3, NEXTCLADE CLI 1.2.1, NEXTALIGN CLI 1.2.1 (2021-08-10)

[BUG FIX] INCORRECT RANGES IN "SNP CLUSTERS" QC RULE

"SNP clusters" QC rule could sometimes produce ranges of SNP clusters with
incorrect boundaries (begin/end). This is now fixed.

[BUG FIX] CRASH WITH INCORRECT COLORINGS IN THE INPUT REFERENCE TREE

Fixed a rare crash in Nextclade CLI and Nextclade Web when input reference tree
contained incorrect fields in "colorings" section of the tree JSON file.

[CHANGE] CLEANUP THE TREE NODE INFO DIALOG

Removed redundant text entries in the tree node info dialog (when clicking on a
node in the tree view). All these entries are still presented in the results
table.

[CHANGE] CLEANUP THE TREE NODE INFO DIALOG

Improved wording of the message in the "Private mutations" QC rule tooltip.

[CHANGE] NEW DOCKER CONTAINER IMAGES FOR NEXTCLADE CLI AND NEXTALIGN CLI

New Docker images are available based on Debian 10 and Alpine 3.14. Debian
images contain a set of basic utilities, such as bash, curl and wget, to
facilitate usage in workflows.

You can choose to use the latest available version (:latest or no tag), or to
freeze a specific version (e.g. :1.2.1) or only major version (e.g. :1), or a
base image (e.g. :debian) or both version and base image (:1.2.1-debian), or mix
and match.

Tag :latest now points to :debian. For previous behavior, where :latest tag
pointed to FROM scratch image, use tag :scratch.

Full list of tags is below.

Image based on Debian 10 is tagged:

nextstrain/nextclade
nextstrain/nextclade:latest
nextstrain/nextclade:1
nextstrain/nextclade:1.2.1

nextstrain/nextclade:debian
nextstrain/nextclade:latest-debian
nextstrain/nextclade:1-debian
nextstrain/nextclade:1.2.1-debian


Image based on Alpine 3.14 tagged:

nextstrain/nextclade:alpine
nextstrain/nextclade:latest-alpine
nextstrain/nextclade:1-alpine
nextstrain/nextclade:1.2.1-alpine


Previously default FROM scratch image is tagged:

nextstrain/nextclade:scratch
nextstrain/nextclade:latest-scratch
nextstrain/nextclade:1-scratch
nextstrain/nextclade:1.2.1-scratch



NEXTCLADE WEB 1.5.2 (2021-07-11)

[BUG FIX] WORKAROUNDS FOR SAFARI WEB BROWSER

The following problems are addressed:

 * crash due to Safari requiring incorrect Content Security Policy when using
   WebAssembly modules (see issue #476)
 * results table and tree not being displayed correctly or at all, due to
   flexbox layout bugs in older versions of Safari

These patches only affect users of Safari web browser, and should not affect
other users.

Despite these fixes, for best experience and speed, we still recommend using
Nextclade with Chrome or Firefox web browsers instead of Safari.


NEXTCLADE WEB 1.5.1 (2021-07-08)

[BUG FIX] BETTER CLADE ASSIGNMENT

In this release we updated the default reference tree. The previous tree had
several basal 20A branches misplaced in clade 20C, resulting in incorrect clade
calls. The new tree addresses this issue and generally improves the quality of
the tree by removing outlier sequences. Nextclade Web already have the new tree,
and users of Nextclade CLI are encouraged to download and use the new tree.json.


NEXTCLADE WEB 1.5.0 (2021-07-01)

[NEW FEATURE] NEW SARS-COV-2 CLADES: 21G (LAMBDA) AND 21H

The updated default SARS-CoV-2 reference tree now contains the recently named
Nextstrain clades 21G (Lambda) and 21H, corresponding to Pango lineage C.31 and
B.1.621. This allows Nextclade Web to detect these clades. Users of Nextclade
CLI are encouraged to download and use the new tree.json.

Note, that gene ORF3a of clade 21H has a 4-base deletion towards the end of the
coding sequence, resulting in a frameshift and a protein truncation. This
frameshift is currently flagged as a potential QC issue though it likely is
biological (present in the viral genome).

[CHANGE] ADJUSTED QUALITY CONTROL (QC) SCORES FOR "FRAME SHIFTS" (F) AND "STOP
CODONS" (S) RULES

We adjusted QC score calculation for "Stop codons" and "Frame shifts" rules,
such that each detection (of a misplaced stop codon or a frame shift,
respectively) results in adding 75 to the score (the higher the score the
worse). This lowers the score for sequences with only 1 frame shift and 1 stop
codon. This is to account for the findings is clade 21H, as described above.

[BUG FIX] REMOVED UNSEQUENCED REGIONS OF LENGTH 0

We fixed a bug where the empty unsequenced regions on either ends of a fully
sequenced sample, were incorrectly displayed as ranges of length 1 in nucleotide
sequence view. Now, in case of full sequences, there will be no unsequenced
areas drawn, as expected.


NEXTCLADE WEB 1.4.0, NEXTCLADE CLI 1.2.0, NEXTALIGN CLI 1.2.0 (2021-06-24)


NEXTCLADE WEB AND NEXTCLADE CLI

[NEW FEATURE] QUALITY CONTROL (QC) RULES: "FRAME SHIFTS" (F) AND "STOP CODONS"
(S)

We have added two additional QC rules designed to flag sequences that likely do
not correspond to functional viruses.

"STOP CODONS" RULE (S)

Checks if any of genes have premature stop codons. A stop codon within a gene
will now result in a QC warning, unless it is one of the very common stop codons
in ORF8 at positions 27 or 68. This list of ignored stop codons is defined in
the stopCodons.ignoredStopCodons property of the QC configuration file (qc.json)
and can be adjusted. The default list might be extended in the future.

Results of this check are available in JSON, CSV, and TSV output files as
qc.stopCodons. In Nextclade Web it is displayed in the "QC" column of the
results table as a circle with letter "S" in it.

"FRAME SHIFTS" RULE (F)

Checks and reports if any of the genes have a length that is not divisible by 3.
If at least one such gene length is detected, the check is considered "bad".
Failure of this check means that the gene likely fails to translate.

Results of this check are available in JSON, CSV, and TSV output files as
qc.frameShifts. In Nextclade Web it is displayed in the "QC" column of the
results table as a circle with letter "F" in it.

[CHANGE] QUALITY CONTROL (QC) CONFIGURATION FILE UPDATED

New entries were added to the QC configuration file (qc.json) for the two new
rules. For Nextclade CLI users, we recommend to download the new file from our
data/ directory on GitHub.

This file is now versioned using the new schemaVersion property. If the version
of qc.json is less than the version of Nextclade CLI itself, users will now
receive a warning.

All QC checks are now optional: a rule that has no corresponding config object
is automatically disabled.

[BUG FIX] CSV/TSV OUTPUT FILES CORRECTED

This release corrects a few issues with CSV/TSV output files:

 * quotation marks are now escaped correctly
 * special characters are now surrounded with quotes
 * line breaks are now encoded as CR LF for better compatibility and consistency
   with Nextclade 0.x
 * column shifts are now prevented in CSV/TSV results when some of the QC checks
   are disabled, as disabled checks return empty strings as result


NEXTCLADE WEB

[BUG FIX] RANGES DISPLAYED OFF-BY-ONE IN GUI

Ranges displayed in Nextclade Web were off-by-one due to a front-end bug. Ends
of ranges (right boundaries) were extending one unit too far. This means that
alignment ranges, missing nucleotide ranges, ranges of gaps, not-sequenced
ranges, were all displayed 1 unit longer than they should have been be. This
release fixes this problem.

Only the display in the results table of Nextclade Web is affected. None of the
output files, either produced by Nextclade CLI or by Nextclade Web are affected.

[NEW FEATURE] INSERTIONS DISPLAYED IN THE RESULTS TABLE

A new column for insertions (abbreviated as "Ins.") was added to the results
table of Nextclade Web. It shows the total number of inserted nucleotides.
Hovering reveals more details about each insertion. This information was already
available in the output files, and is now also shown in the GUI.


NEXTALIGN CLI

There are no changes in Nextalign in this release, but we keep versions of
Nextalign and Nextclade in sync.


NEXTCLADE WEB 1.3.0, NEXTCLADE CLI 1.1.0, NEXTALIGN CLI 1.1.0 (2021-06-22)

This series of releases adds a new output file nextclade.errors.csv to all tools
and adds the output file nextclade.insertions.csv to Nextclade Web (it has
already been available for users of CLI tools).

nextclade.insertions.csv contains information about insertions in the following
columns: seqName, insertions. The column insertions contains a list of
nucleotide insertion entries delimited by semicolon. Each nucleotide insertion
entry consists of the position of the first nucleotide and the inserted
fragment, delimited by colon.

nextclade.errors.csv contains information about errors, warnings and gene
processing failures in the following columns: seqName, errors, warnings,
failedGenes. All lists are semicolon-delimited.

In both files, each row corresponds to one sequence, identified by seqName.


1.2.0 (2021-06-21)


NEXTCLADE WEB APPLICATION

In this release we improve how low-memory conditions are handled in the
Nextclade web application. From now on, when Nextclade runs out of system memory
(RAM), you will receive an extensive error message with a list of possible ways
to address the issue.

A settings dialog was added, allowing the user to change the number of CPU
threads. It can be opened using the new "Settings" button on the top panel. In
Chrome and other Chromium-based browsers (Edge, Brave, etc.) the dialog also
displays the amount of memory available and on this basis provides a suggestion
for the number of CPU threads for optimal performance.

Note that these user settings persist across browsing sessions, Nextclade runs,
page refreshes and Nextclade version updates.


1.1.0 (2021-06-15)


NEXTCLADE WEB APPLICATION

This release makes gene translation failures more apparent in Nextclade Web
application.

Previously, when a gene failed to be translated, Nextclade showed a blank row in
the gene view in the results table and it was hard to understand whether there
were no aminoacid changes or the translation had failed. Now, these rows will be
colored in dark gray, contain a message, and some detailed information in the
tooltip.

This should hopefully make it clearer which genes are missing from the results
and why.


1.0.1 (2021-06-12)


NEXTCLADE WEB APPLICATION

This release fixes a problem in Nextclade web application where non-fatal errors
during sequence processing (such as sequence alignment failures) were crashing
the whole application, displaying an error dialog window.

Now sequence analysis errors are reported right in the table, as before.

Thanks Joan Gibert (@Tato14) for the bug report (#434)


1.0.0 (2021-06-11)

This major release brings many new features and bug fixes.

We release new versions of all of the tools in Nextclade family: Nextclade web
application, Nextclade CLI and Nextalign CLI.

> With this major release we introduce breaking changes. In particular, changes
> to input and output file formats as well as to arguments of command-line
> tools. The breaking changes are marked with "💥 BREAKING CHANGE" prefix. It is
> recommended to review these changes.

Below is a description of changes compared to version 0.14.4.


GENERAL

Changes that affect all tools:

 * The underlying algorithm has been completely rewritten in C++ (versions 0.x
   were implemented in JavaScript), to make it faster, more reliable and to
   produce better results. Web application now uses WebAssembly modules to be
   able to run the algorithm.

 * 💥 BREAKING CHANGE: Nextclade now uses Nextalign algorithm for the alignment
   and translation of sequences. This means that nucleotide alignment is now
   aware of codon boundaries. Alignment results and some of the analysis results
   might be slightly different, depending on input sequences.

 * Similarly to Nextalign, Nextclade can now output aligned peptides. In
   general, Nextclade is a superset of Nextalign and can do everything Nextalign
   can, plus more (for the price of additional computation).

 * 💥 BREAKING CHANGE: Gene maps are now only accepted in GFF3 format. See an
   example at GitHub. Migration path: use provided default gene map or convert
   your custom gene map to GFF3 format.

 * 💥 BREAKING CHANGE: JSON results file format has changed. It now contains an
   object instead of an array as a root element. The array of results is now
   attached to the results property of the root object. Migration path: instead
   of using output array directly use output.results now.

 * 💥 BREAKING CHANGE: JSON fields and CSV/TSV columns totalMutations and
   totalGaps were renamed to totalSubstitutions and totalDeletions, for
   consistency. Migration path: use new JSON property or column names.


NEXTCLADE WEB APPLICATION V1

Web application mostly maintains it previous interface, with small improvements
and with adjustments to the new underlying algorithm implementation.

 * New "Download" dialog was introduced, which replaces the old "Export"
   dropdown menu. It can be toggled by clicking on "Download" button on
   "results" page.

 * Aligned sequences now can be downloaded in the new "Download" dialog.

 * Translated aligned peptides now can be downloaded in the new "Download"
   dialog.

 * "Sequence view" column of the results table now can be switched between
   "Nucleotide sequence" view and "Gene" view. In "Gene" view, aminoacid
   mutations and deletions are displayed for a particular gene.

 * "Sequence view" can also be switched by clicking on a gene in "Genome
   annotation" panel below the results table.

 * Results table tooltips has been cleaned up, information was spread between
   corresponding columns, in order to fit the tooltips fully to common screen
   sizes. For example, list of mutations is now only available when mouse over
   the "Mut." column.

 * The tooltips to explore diversity have become much more informative. For
   amino acid changes, we now provide a nucleotide context view that is
   particularly helpful for complex mutations. Consecutive changes are merged
   into one tooltip.


NEXTCLADE CLI V1

Nextclade CLI v1 is a replacement for Nextclade CLI v0. It is recommended for
advanced users, batch processing and for integration into pipelines.

 * Nextclade CLI 1.0.0 is available on GitHub Releases and on DockerHub:

 * Node.js is no longer required. Nextclade is now distributed as a standalone
   native executable file and is ready to be used after download. The latest
   version is available for major platforms at Github Releases page.

 * The limitation of Node.js on maximum input file size (500 MB) is now removed.
   Nextclade should be able to handle large files and to use I/O resources more
   efficiently. Nextclade will stream sequence data to reduce memory
   consumption.

 * Nextclade CLI is much faster now. Depending on conditions, we measured
   speedups up to 5x compared to the old implementation.

 * 💥 BREAKING CHANGE: Nextclade no longer includes any default data. The
   following flags for input files were previously optional but are now
   required: --input-root-seq, --input-tree, --input-qc-config. The
   --input-gene-map flag is optional, but is highly recommended, because without
   gene map, the alignment will not be informed by codon boundaries and
   translation, peptide output and aminoacid change detection will not be
   available. The example SARS-CoV-2 data can be downloaded from GitHub and used
   as a starting point. Refer to built-in help for more details (--help).
   Migration path: download the default data add new flags if you you were
   previously not using them.

 * 💥 BREAKING CHANGE: Reference (root) sequence is no longer being written into
   outputs by default. Add --include-reference flag to include it. Reference
   peptides will also be included in this case. Migration path: use the
   mentioned flag if you need reference sequence results included into the
   outputs.

 * 💥 BREAKING CHANGE: Nextclade might write aligned sequences into output files
   in the order that is different from the order of sequences in the input file.
   If order is important, use flag --in-order to enforce the initial order of
   sequences. This results in a small runtime performance penalty. Refer to
   built-in help for more details (--help). Migration path: use the mentioned
   flag if you need results to be written in order.


NEXTALIGN CLI V1

Nextalign is a new tool that contains only the alignment and translation part of
the algorithm, without sequence analysis, quality control, tree placement or
other features of Nextclade (making it faster). It is available on Github
Releases page. Refer to built-in help for more details (--help).


DEPRECATION OF NEXTCLADE CLI V0

 * Nextclade CLI 0.x is now deprecated and not recommended for general use. We
   recommend all users to migrate to version 1.x. Old versions will still be
   available on NPM and Docker Hub, but there are no plans to release new
   versions. Please reach out to developers if you still need support for
   versions 0.x.

 * Container images hosted on Docker Hub will now resolve to Nextclade family
   v1. In order to pull the version of family 0.x, use tag :0 or a full version
   explicitly, for example :0.14.4:
   
   docker pull nextstrain/nextclade:0
   docker pull nextstrain/nextclade:0.14.4
   

We hope you enjoy the new release and as always, don't hesitate to reach out to
Nextstrain team on Nextstrain discussion forums or on GitHub.


0.14.4 (2021-06-07)

This version updates the default SARS-CoV-2 reference tree with new Nextstrain
clade designations and alias names for the WHO VoC and VoI names, so that
Nextclade now can detect these clades.

See also:

 * Original change in Nextstrain: nextstrain/ncov#650

 * Current clade definitions in Nextstrain: clades.tsv

 * World Health Organization: Tracking SARS-CoV-2 variants


0.14.3 (2021-05-20)

The default SARS-CoV-2 reference tree is updated. It allows Nextclade to detect
the new Nextstrain clade 21A.

See also:

 * Current Nextstrain SARS-CoV-2 clade definitions in nextstrain/ncov GitHub
   repository: clades.tsv

 * Clade 21A in Nextstrain global build: link

 * Variant 21A/S:154K on CoVariants.org: link

 * Variant 21A/S:478K on CoVariants.org: link


0.14.2 (2021-03-30)

We updated Nextstrain Auspice (the tree renderer) from version 2.18.2 to version
2.23.0, with bug fixes and new features. In particular, the filtering
functionality is now similar to what can be found on nextstrain.org. We now
color the tree by clade and filter by node type ("reference" vs "new" nodes).
See Auspice changelog for more details.

In other news, Nextalign 0.2.0 is now available. See Nextalign changelog on
GitHub Releases page.


BUG FIXES

 * account for the fact that the length of the gene can be different from %3
   before stripping (6fc99a0)
 * ensure backwards compatibility with the old GFF parser (07156b7)
 * ensure GFF3 spec compliance of gene map parser (2355d3d)
 * integer underflow in parallelism parameter to tbb pipeline (42664e7)
 * prevent local variable shadowing (64c5661)
 * prevent potential out-of-bounds array access (4663b32)
 * query results are returned as alignment with insertions stripped, hence gap
   symbols in the reference should be stripped (01e8628)
 * remove erroneous check for length%3==0 before gap removal (d95761d)


FEATURES

 * add more tree filtering criteria (d852122)
 * add tree filtering from auspice (27eb67e)
 * add tree filters summary (67c671e)
 * adjust help text and default flags for new data location (27fd88e)
 * color tree by clade and filter by Node Type - New by default (79de7cd)
 * output aligned reference sequence, make ref outputs optional (49da3f5)
 * remove old tree filter panel (13af3ad)
 * remove separate reference sequence output file (5a899e2)
 * rename flag --write-ref to --include-reference (36c52e9)
 * upgrade auspice to 2.23.0 (276675b)


0.14.1 (2021-03-12)

This release of Nextclade adjusts the default Quality Control configuration to
account for ever-increasing diversity of circulating SARS-CoV-2. The following
default QC parameters have been changed:

Rule "Private mutations":

 * "typical" (expected number of mutations) increased from 5 to 8
 * "cutoff" (number of mutations to trigger QC warning) increased from 15 to 24

Rule "Mutation clusters":

 * "clusterCutOff" (number of mutations within window to trigger a warning)
   increased from 4 to 6

As always, users can provide their own QC configuration, to override the
defaults, if these changes are not desirable.

Additionally, Nextalign 0.1.7 is now available, which fixes rare crash in
peptide alignment, when a low-quality sequence has not enough seed positions.

Don't hesitate to provide feedback, report issues and share ideas on GitHub.


BUG FIXES

 * prevent crashing when not enough good gene seed positions (6233aa2)

Misc:

 * relax SARS-CoV-2 QC parameters to account for increasing diversity of
   circulating virus


0.14.0 (2021-03-08)

This is a maintenance release which updates the default reference tree with more
recent genomes and increases the number of sequences in it to better reflect
circulating diversity.

Additionally, we extend our list of partial codon patches (first introduced in
version 0.12.0), in order to correctly detect deletions involving spike protein
positions 141 and 142.

There are also some small improvements in the user interface.

As always, don't hesitate to provide feedback, report issues and share ideas on
GitHub.

The full list of changes is below.


BUG FIXES

 * add additional directions to patch partial codons (d266fa7)
 * Correct Node.js version requirement for the Nextclade CLI (24c7b76)
 * don't attempt to create directories from empty paths (576eb9f)
 * increase clade column width to accommodate longer clade names (557d3d2)


0.13.0 (2021-02-17)


🚀 ANNOUNCING NEXTALIGN

Today we announce Nextalign, the new command-line tool and the algorithm for
viral genome alignment.

Nextalign is based on the alignment algorithm used in Nextclade, ported to C++
and made into the standalone command-line tool. Nextalign development is
currently primarily focused on SARS-CoV-2, but it can be used with any virus
(and if you encounter any difficulties, let us know on GitHub).

There are 2 ways of using Nextalign:

 * Download Nextalign on Nextclade Github Releases page to run natively

 * Use Docker container image: nextstrain/nextalign
   
   docker run -it --rm nextstrain/nextalign:latest --help
   

Learn more about Nextalign here.


💥 [BREAKING CHANGE] NEXTCLADE HAS MOVED!

Once started as a prototype project at NeherLab, Nextclade is a part of
Nextstrain project for some time now. For consistency, we will now publish
Nextclade in Nexstrain-branded NPM and DockerHub repositories:

 * NPM: @nextstrain/nextclade

 * DockerHub: nextstrain/nextclade

We added a "Downloads" section on the main page of Nextclade web application.
Additionally, this release contains a few fixes to website's look & feel and
slightly improves user experience on mobile devices.


BUG FIXES

 * accept 0-based frames as per gff spec (5c3af28)
 * adjust test expectations to new default parameters (9a457c3)
 * center main page content properly (460464d)
 * check for length being a multiple of 3 before codon aware stripping (a33dd6b)
 * correct error message formatting (016e924)
 * correct gene length check (c6e488f)
 * end of gene in gene extraction and cli logging (16626fa)
 * fix non-responsive elements on main page (36fa501)
 * only protect gaps on the edges (fef98c0)
 * pass gff filename to csv parser for more descriptive errors (6843cc2)
 * pass the score-gap-open-out-of-frame option from cli into lib (f9a435d)
 * remove excessive padding around upload box (34e7bce)
 * remove gap under the footer (d4db78b)
 * remove horizontal overflow from main page (d1061f5)
 * throw error when stripped sequence has zero length (2b74257)


FEATURES

 * add an option to allow out-of-order writes (22702e3)
 * add downloads section to nextclade main page (96bd007)
 * add in-order CLI flag and make out-of-order behavior the default (e722504)
 * add logger with configurable verbosity (0a62c1f)
 * add team portraits to main page (7566b27)
 * add validation for numeric cli params (3915334)
 * adjust team credits styling and text (ba7f0ab)
 * clarify descriptions for score-gap-open* family of cli options (3765de8)
 * differentiate gap open cost outside of genes, in frame, and out of frame
   (a5ead08)
 * don't use frame from gff (d9f3023)
 * expose nextalign algorithm params in cli (852c2b1)
 * expose nextalign algorithm params in library (5e3900a)
 * extend cli param descriptions (a4ac1d5)
 * extend project description (30d104e)
 * further improve logging (2f593f0)
 * improve warning messages during gene extraction (07e2c38)
 * limit clade schema size (a75dace)
 * rename negative 'scores' to 'penalties' (17bb582)
 * skip minimal sequence length check for aminoacid alignment (394ca8e)
 * validate codon-related penalty scores only if genes are provided (9627cfc)


0.12.0 (2021-01-21)

This release provides a temporary solution for the problem when certain
aminoacid deletions are not being detected properly.

We now maintain a list of "patches" to selectively modify the sequence during
translation: the partial codons at the beginning and end of the deletion are
combined to one complete codon. This way, deletions that start within a codon no
longer result in invalid peptides, and some of the well-known deletions are now
properly recognized.

See pull request #308

Thanks @bede, @dbrandtner, @giuseppina950, @iskandr, @SarahNadeau for their
reports.

At the same time we are working on a more permanent solution.

Please report issues and leave feedback on GitHub


BUG FIXES

 * rename variable and fix condition (40ba67f)


FEATURES

 * allow codon padding to happen forward and backward for custom cases (945ca77)
 * properly translate out-of-frame gaps (c34a640)
 * refactor the codon patching by gene and deletion start: (7e258d8)


0.11.2 (2021-01-18)

This release updates default reference tree and adds new clade designations.

Additionally, it fixes a problem of excess divergence in cases where there are
gaps in the reference node we attach to. These gaps no longer contribute to
divergence.


BUG FIXES

 * avoid counting every gap in a new node as one divergence unit (51bfce6)


0.11.1 (2021-01-07)

BREAKING CHANGE: Starting with this version Nextclade uses the new Nextstrain
clade definitions for SARS-CoV-2. "What are the clades?" section on the main
page was updated accordingly. For more information on the updated clade
definitions, see our blog post.

Additionally, Nextclade alignment algorithm was adjusted to correctly handle a
few more corner cases. In particular, seed matching was improved to:

 * avoid stretches of N when choosing seeds
 * increase the number of seeds

The trimming of terminal N characters (introduced in 0.10.1) was removed,
because the new improvements also handle this case.

Thanks Stacia K Wyman and Syed Muktadir Al Sium for the bug reports!

See also: issue #288 See also: issue #290


BUG FIXES

 * actually use the map to good characters (c3a0a2c)
 * remove old clades (43f3c86)


FEATURES

 * add new clade schema (5ab7054)
 * improve seed matching by logging good nucleotides (ce62478)
 * increase number of seeds and reduce redundant seed search (d1e0a2f)
 * update SARSCoV2 tree.json (880223e)


0.10.1 (2020-12-30)

This release fixes a problem with input sequences with large chunks of N
nucleotides at the edges. To ensure correctness of results, before alignment we
now trim contiguous blocks of Ns at the beginning and at the end of each
sequence.

Thanks Stacia K Wyman for the bug report.

See also: issue #285


BUG FIXES

 * trim leading and trailing to void seed matching problems (17a554a)


0.10.0 (2020-12-21)

Nextclade (both, web and CLI versions) no longer uses or requires the standalone
gene map file by default. Instead, it takes the corresponding information from
genome_annotations field of the reference tree file (nowadays, this property is
usually present in all Auspice JSON v2 files produced with Nextstrain's Augur).
A standalone gene map file can still be provided, in which case it overrides the
gene map found in the reference tree file.

In some cases, when there were multiple mutations in the same codon, Nextclade
has been reporting aminoacid changes incorrectly, as if these changes were in
separate codons having the same position. The reported changes would then list
this aminoacid mutation twice, with the same position, but with two different
resulting aminoacids (which is impossible). We adjusted the detection of
aminoacid changes by performing full translation of every gene, so this issue is
now fixed.

Nexclade now also reports aminoacid deletions. It no longer outputs
aminoacidChanges field/column in JSON, CSV and TSV exports. Instead, it outputs
separate aaSubstitutions and aaDeletions columns.

Nexclade is now better suited for the analysis of viruses other than SARS-CoV-2.
We briefly tested it with the Flu virus, however, more testing is required.
Please reach out to developers if you are interested in the analysis of other
viruses.

The default reference tree has been updated.


BUG FIXES

 * add download location and local rules (fbf6adc)
 * add reversion mutation to distance of attached tree nodes (0889457)
 * avoid buffer overflow by using positions relative to the gene start (faf2a88)
 * convert gene map to zero-based indices (02b8b8e)
 * corect the nuc position calculation relative to gene start (97e4508)
 * correct deletion range end (23b794c)
 * ensure only full-codon nuc dels are associated with the aa dels (0448d1f)
 * exclude aa deletions from aa substitutions (bc188bd)
 * fix arguments to intersection in aa Association (b75ff5c)
 * make sure query gene changes don't propagate to the ref gene (61b9bf5)
 * make sure the gene ranges are semi-open (3d9754a)
 * make sure the genes of the gene map are of correct length (a737a5e)
 * only count nucleotide substitutions towards divergence during tree attachment
   (2f2305d)
 * rectify codon position calculation (1e56a18)
 * revise clade names (79541b4)
 * revise clade names (88e612d)
 * update genome size when custom root sequence is provided (680e44c)


FEATURES

 * adapt filtering UI for the new aa subs and dels (db97f2b)
 * adapt results serialization for the new aa subs and dels (2be7de6)
 * adapt results table UI for the new aa subs and dels (89e40be)
 * add aa deletions to the tree tooltips (613971e)
 * add additional checks when loading gene map (1d39b4e)
 * add codons to the aa change objects (d425981)
 * add subclades (24b0abc)
 * guess unit of measurement of divergence (8db8bde)
 * improve reporting of bad codons (66fc002)
 * list partial codons as mutations to X (16e11d9)
 * re-associate nuc changes with their corresponding aa changes (cc17a97)
 * reimplement aminoacid changes extraction, extract deletions (7472109)
 * take gene map from tree json (9466d8f)
 * truncate aminoacid changes lists in tooltips (a383b4c)


0.9.0 (2020-12-02)

This release is focused on advanced users of Nextclade web application. On the
main page you can find the new "Advanced mode" toggle, which opens access to the
additional parameters. There you can set custom input data: reference tree, root
sequences, QC parameters, and PCR primers. For each filed you can provide a
local file, a URL to a remote file, or paste the data into the text box
directly. Parameters that are left blank will be substituted from Nextclade's
defaults. All data formats are shared with the command-line version of Nextclade
CLI.

You can find the full list of changes below:


BUG FIXES

 * avoid passing the DOM button click event to state (6fb21de)
 * correct grammar (dd8f5af)
 * don't pass the custom props to DOM nodes (cea8285)
 * don't pass the custom props to DOM nodes (more) (47b6fe0)
 * don't pass the custom props to DOM nodes (more) (585642b)
 * remove delay in navigation to results page when after file loaded (855e285)


FEATURES

 * add advanced mode toggle (da3e3d8)
 * add badges indicating default input state (b6078fd)
 * add button and modal to create new runs (f3b4f72)
 * add mockup of advanced controls on main page (31a3b30)
 * add placeholder for previous results section (5260682)
 * add tooltip text for the run button (5ba07ee)
 * add tooltips and visual helpers to improve file picker ux (666a842)
 * align file picker header text (5ff6eb5)
 * bail out of data processing early on fetch failure from url params (6e5b9a4)
 * center-align text (fa72701)
 * connect input controls to new input param state (5744fcb)
 * customize instruction and placeholder text on url and paste comps. (2adbd92)
 * dim placeholder text color (6585a10)
 * disable virus selection dropdown and add a tooltip for it (d3024c5)
 * fetch inputs from user-provided URL (e352814)
 * handle errors in simple mode better (417b11c)
 * improve file picker layout (6e99fbb)
 * improve layout of main page (29b99ef)
 * improve layout of network error messages, clarify the text (fd18f34)
 * improve layout of tab-cards and URL tab body (7775325)
 * improve layout of the "paste" tab panel (d111a96)
 * improve layout of the "url" tab panel (a3eed14)
 * improve layout of the file info component (407fcd7)
 * improve layout of upload cards (18a49c8)
 * improve network error messages (08f3f5f)
 * improve uplolader text for case where data is provided as a string (7f29bf4)
 * increase feature box height (9777ae6)
 * increase file picker height (1933511)
 * indicate file upload with status text (c40a76d)
 * launch algorithm on "Run" button click in advanced mode (84afce2)
 * load and process files in advanced mode (fbb106c)
 * make file pickers collapsible (c51b4f8)
 * reduce spacing between cards (9a94b51)
 * run automatically after example data is loaded (d0c07d5)
 * run immediately after input is provided in simple mode (5d68c73)
 * show error alerts under file dialogs when there are errors (6aa42be)
 * soften card shadows (b50d2ee)
 * use new file picker in simple mode too (9344d92)
 * wrap text in text area for pasting sequences (73540c5)


0.8.1 (2020-11-12)

This is a follow-up release, on top of version 0.8.0.

In this version Nextclade further improves handling of gaps in node distance
calculation.

We increased the thresholds of private mutations in Quality Control calculation
for SARS-CoV-2, to account for the current situation, so some sequences will
have better QC scores now. As usual, you can set the desired custom values in
Settings dialog or using the --input-qc-config flag in the command-line version.

Additionally, this version introduces some minor improvements in the user
interface as well as in runtime performance.

You can find the full set of changes below:


BUG FIXES

 * formatting markdown snippets (about and changelog) (b8b1971)
 * increase allowed private mutations -- as SARS-CoV-2 diversifies, sequences
   are expected to have more private mutations (fc1e885)


FEATURES

 * exclude gaps from private mutations counting (5b04903)
 * only show the "what's new" popup on major branches (a902c6a)


PERFORMANCE IMPROVEMENTS

 * avoid re-filtering gaps from mutations for every node every time (0509770)
 * catch common cases in nucleotide match function before doing full set
   intersection (20a20ae)


0.8.0 (2020-11-10)

This release brings several important bugfixes, improvements and new features.

In this version Nextclade adds support for the new SARS-CoV-2 regional
subclades. The default reference tree now contains a few nodes with clades
20A.EU1 and 20A.EU2. For more information about the new variants refer to
Hodcroft et al., 2020.

Nextclade algorithms now handle ambiguous nucleotides and gaps in the reference
tree and the root sequence. Previously this was not needed, because our default
root sequence is always full and unambiguous, but this is important now that
Nextclade allows custom root sequences.

Nextclade developers will no longer maintain clades.json file with a list of
clades. Since v0.4.0, clade assignment is performed by taking clade of the
nearest node on the reference tree, so the algorithm does not depend on this
file. This change means that users no longer have to provide clades.json for
custom viruses anymore, but also that the "Gene map" panel in the web
application will not show markers for clade-defining mutations.

Nextclade web app now includes more interesting and relevant example SARS-CoV-2
sequences to better showcase application's features.

Nextclade web application now accepts new URL parameters. Additionally to
input-fasta= parameter to download and start processing a given FASTA file
(introduced in v0.7.0), you can now also provide input-root-seq= parameter to
download and use a given custom root sequence, as well as input-tree= parameter
for a custom reference tree.

You can now export the resulting tree in Auspice JSON v2 format, with the
analyzed sequences placed onto the reference tree. Check the "Export" dropdown
on the results page. This file can then be used for further analysis or
visualization (for example with auspice.us).

> ⚠️ Exercise caution when interpreting Auspice JSON v2 file generated by
> Nextclade. Nextclade's algorithms are only meant for quick assessment of
> sequences: they perform quality control, clade assignment, and a simple
> phylogenetic placement. Nextclade is not a replacement for the full
> phylogenetic analysis with the main Nextstrain pipeline.

The non-algorithm part of the command-line version of Nextclade has been
substantially rewritten. It now takes advantage of all processor cores in the
system. You can set the desired level of parallelism with the new flag: --jobs.
Additionally, sequences that trigger processing errors are now included into
CSV, TSV and JSON output files, along with their respective error messages (in
the new errors column).

The redundant column qc.seqName has been removed from CSV and TSV results. Use
column seqName instead. The order of columns has been changed, to emphasize
clades and QC results.

There are more minor fixes and improvements. Here is a full list of changes
since previous release:


BUG FIXES

 * ensure auspice strings interpolate correctly (1f0e3c1)
 * remove black overlay above entropy panel when holding shift or alt (fbc851c)
 * ensure isMatch handles ambiguous nucleotides in both reference and query
   (ee35f77)
 * exclude gaps in reference node from distance calculations (8e6571c)
 * use consistent line endings in json export (3d8ddb5)
 * ensure isMatch handles ambiguous nucleotides in both reference and query
   (ee35f77)
 * exclude gaps in reference node from distance calculations (8e6571c)
 * cli: add missing files into docker builds (dbb54f2)
 * cli: preserve failed sequences in results (8e1e78b)


FEATURES

 * cli: add jobs flag for setting the level of parallelism (96100b6)
 * cli: don't finalize tree when tree output is not requested (8a9c767)
 * cli: make CLI run in parallel (5a8902c)
 * add "what's new" popup, optionally show on every release (66cf03d)
 * allow exporting Auspice tree json result again (5428bc8)
 * enforce csv column order, remove duplicate qc.seqName column (5928b53)
 * feat!: remove clade markers from Gene Map, remove clades.json (858b92a)
 * feat: add more interesting example data
 * feat: add rule to augur workflow to make example sequence fasta
 * feat: add subclades
 * fetch input root sequence and input ref tree provided URL params (585371a)
 * remove uppercase text transform from buttons (79c99b6)
 * use the root sequence and tree provided in the URL (d364efa)


BREAKING CHANGES

 * We removed clades.json file and modified Virus data structure. For a while
   now we assign clades by looking at the closest node in the tree, and we don't
   rely algorithmically on clade definitions in clades.json. The only place
   where clade definitions were used is displaying clade-defining mutation
   markers on Gene Map. We agreed that with introduction of subclades we want to
   remove clades.json, rather than update it. It also means removing
   clade-defining mutation markers on Gene Map in the web app. This commit makes
   this happen.
 * qc.seqName is removed from CSV, TSV and JSON outputs (it had the same values
   as seqName)
 * order of columns is changed in CSV ans TSV outputs


0.7.8 (2020-11-05)

This is a bugfix release which addresses CLI crash due to improper reading of
the custom gene maps


BUG FIXES

 * cli: add missing preprocessing step for custom gene maps in CLI (0fb31dd),
   closes #252


0.7.7

This is a bugfix release which addresses a rarely occurring situation when clade
is incorrectly assigned due to a defect in the clade assignment algorithm.


BUG FIXES

 * remove mutually cancelling mutations during tree preprocessing (a420e83)


0.7.6 (2020-10-27)

This is a bugfix release which addresses crash of the web application which
occurred when removing a tree filter by clicking on a "cross" icon of the filter
badge.

Additionally, we decided tp force reset all users' browsers to use English
version of the Nextclade web application, because other locales went out of sync
significantly. P.S. We are looking for translators!


BUG FIXES

 * avoid crash on filter badge removal (472b9ab), closes #235


FEATURES

 * force reset all users to English locale (762d34d)


0.7.5 (2020-10-06)

This release removes nucleotide composition from CSV and TSV outputs. Due to
variations of the alphabet, nucleotide composition has been adding and removing
columns unpredictably. By removing it we opt-in to a stable set of columns.


FEATURES

 * don't output nucleotide composition to CSV (ff7c883)


0.7.4 (2020-10-05)

This is a bugfix release which addresses improperly formatted SNP clusters in
output files


BUG FIXES

 * format SNP clusters properly for export (c7aa5c7)


0.7.3 (2020-10-05)

This is a bugfix release


BUG FIXES

 * add last newline in exports (c3d83d6)
 * prevent app from crashing when a locale is missing (1fd2a19)


0.7.2 (2020-10-01)

This version introduces a mechanism that allows Nexclade to signal common ad
blocking browser extensions that it respects privacy. We hope that it may
increase compatibility when these extensions are enabled.


FEATURES

 * attempt to reduce breakage by adblockers (1870cdc)
 * warn about possible adblocker interference (ffff5fb)


0.7.0 (2020-10-01)

Nextclade 0.7.0 ships with new CLI flags, allowing overriding most of the
virus-specific parameters:

--input-fasta
--input-root-seq
--input-tree
--input-qc-config
--input-gene-map
--input-pcr-primers


Additionally, the web application now can fetch a .fasta file from a remote
location using input-fasta query parameter:
https://clades.nextstrain.org/?input-fasta=<your_url> (CORS needs to be enabled
on your server)


BUG FIXES

 * ensure example sequences are loading correctly (fc44961)


FEATURES

 * improve network error popup informativeness and looks (ffd2995)
 * cli: add CLI flag to output a CSV with clades only (bb405ff)
 * cli: add possibility to override clades, primers and gene map (643607b)
 * cli: output a TSV with clades only, instead of CSV (d956f0b)
 * deduce virus genome size from root sequence length (22d4e7a)


0.6.0 (2020-09-24)

This a bugfix release which addresses CLI crash on alignment failure


BUG FIXES

 * fix CLI crash on alignment failure (b02a602)


0.5.2 (2020-09-23)


BUG FIXES

 * correct the link URL to nextstrain ncov clades (92982c7)


0.5.1 (2020-09-23)


FEATURES

 * fetch input fasta from a remote location (a339c05)
 * present error message on data fetch failure (aed0a21)


0.5.0 (2020-09-21)


BUG FIXES

 * ensure proper complement and position of ambiguous nucleotides (8de7f5d)
 * remove Charité_NS_RdRp_P primer, correct name of Charité_N_RdRp_P (488bf05)
 * remove trailing spaces from primer sources (8dce5c6)


FEATURES

 * add primer changes to the tree node info (eb51963)
 * add tree coloring by presence of PCR primers (21dceed)
 * convert primer data to JSON (36bbd6e)
 * display PCR primer changes in tooltips (801622f)
 * don't report mutations where primer contains ambiguous nucleotides (7fc5383)
 * format PCR primer changes when preparing CSV export (b9019c5)
 * list primer changes in mutation tooltips on sequence view (98e0189)
 * retry with reverse-complement primer if not found in root sequence (8a7a458)


0.4.6 (2020-09-14)


BUG FIXES

 * attempt to fix tsv extension on chrome mac (e47aa5e)
 * cli: make sure the custom tree is used (d32d7c2)
 * make sure exported files have correct extensions (2bb74c8)
 * cli: make desc casing consistent (976a47d)
 * change app description to match the main page title (43daceb)
 * correct substitutions in translated strings (fa2120a)
 * ensure saved locale is restored on launch (86c1688)


FEATURES

 * cli: add ability to output Auspice JSON v2 in CLI (77563a3)
 * add basic node cli (1eeef0c)
 * add cli arguments for inputs and outputs (db8c44e)
 * add docker container config (8ea7047)
 * add links to cli and a short intro on main page (4a724d9)
 * cli: allow custom root sequence, qc config and ref tree (da5824a)
 * improve fr translation (243bcbf)
 * improve ru translation (64aff1a)
 * remove unused locale keys (82bd7ba)


0.4.0 (2020-09-01)


BUG FIXES

 * add missing word (f15af21)
 * adjust QC filter to new scoring scheme (4129947)
 * adjust reducers, ui and more types for the new results layout (8520daf)
 * avoid unrecoverable failure when a sequence fails to align (1511d7b)
 * disable "show tree" button until full results are available (283dc9e)
 * don't show settings dialog by default (627a5ae)
 * ensure progress bar retains failure state until the end of the run (796eddf)
 * fix incorrect QC status assignment (aff806b)
 * fix more type errors (70fd82a)
 * fix text color on OK button (f8b139d)
 * fix type errors (2108b28)
 * fix typos (cebcdb3)
 * flip erroneous comparison (fe2446b)
 * make sure QC strings on tree nodes are being translated (7c9c96d)
 * make sure to format non-ACGTN ranges for export (75abfc3)
 * make sure tooltips are attached to the right element (2bccf84)
 * make sure tree nodes are properly colored on first tree render (56662fe)
 * make sure we find divergent mutations correctly (6b7be19)
 * make text casing consistent (6de96d2)
 * prevent text from selection on QC status icons (bd2fb9f)
 * dev: fix type error and tests (ea2fef4)
 * remove stray brace (272a44f)
 * remove unused package (23c8e82)
 * type errors in QC runner (ab4d34c)


FEATURES

 * add "phylogenetic placement" feature box, adjust main page styling (45f01fa)
 * add button to rerun the algorithm (a4dbcba)
 * add intermediate QC level (46fd02f)
 * add new QC text to the auspice tree (641ef02)
 * add reversion mutations to the terminalMutations, rename function (f2dc7c2)
 * adjust exports for new data layout, remove auspice json export (05a9409)
 * adjust progress bar for new algorithms (1a15c4c)
 * adjust progress bar to better reflect recent algorithm changes (0562dfa)
 * adjust progress indicator for the new state and event flow (3f3839b)
 * adjust results table for the new state and event flow (3d0c835)
 * adjust sorting and filtering for the new QC categories (7a1d68c)
 * adjust sorting for the new QC results (638750d)
 * assign clade from nearest node in reference tree (d23d5e1)
 * change privateMutation rule to affine linear excess (98c71d6)
 * change QC icon labels (dba62b6)
 * combine scores quadratically such that two scores of 70 trigger a warning, or
   one score of 100 (c543cee)
 * display status for every QC rule as colored circles (637a095)
 * expose QC config in the UI (7fc5881)
 * format QC tooltip based on new results (ba412bb)
 * hide passed QC checks from tooltip (07f92e3)
 * highlight rows with issues (ba3e2ed)
 * improve QC tooltips, improve layout of large tooltips (7716b14)
 * improve string formatting of insertions (c0863e2)
 * list QC rules in the same order (1ad2738)
 * make QC status coloring more consistent (b17b33f)
 * make QC status icons' labels more distinct, single-letter (4350c28)
 * pass mutations difference from reference node to QC (48415c1)
 * prettify QC status circles (ad61a15)
 * reduce weight of missing data check (575aa05)
 * rename variables to clarify intent (389dd79)
 * restyle buttons on results page, adjust for smaller screens (5a4e806)
 * round QC scores in UI (99aaabe)
 * show per-rule QC icons in tooltips (4c45584)
 * simplify QC message for mixed sites (a8228a8)
 * soften QC status icon colors (cadae7e)
 * use new QC status on tree nodes (423d459)
 * dev: implement better error handling in algorithm saga (49c50c2)
 * dev: improve runtime performance profiling (538e82e)
 * dev: setup runtime performance profiling (dd12d48)
 * subtract thresholds when calculating QC scores (7f5013b)
 * tweak MissingData QC rule to return values such that above 100 is problematic
   (8d49eee)
 * tweak parameters of QC rules. remove unused config values (b78b143)


PERFORMANCE IMPROVEMENTS

 * assign all QC results in bulk to avoid redux performance overhead (dced28c)
 * assign clades in bulk to improve performance (6ce4a2e)
 * make object cloning faster (6940e9a)
 * memoize a slow function (92ba87c)
 * memoize slowest React components (4f2969b)


REVERTS

 * Revert "refactor: split tree preparation away from tree algorithm" (2b3df69)


0.3.7 (2020-08-28)


FEATURES

 * add export to tsv (0c4452a)


0.3.6 (2020-08-18)


BUG FIXES

 * lint (521594b)


FEATURES

 * dev: visualize functions in redux devtools (fa8fa54)
 * add ability to disable filters temporarily (a09521c)
 * add auspice entropy widget (96ad6f6)
 * make sure entropy chart renders properly, adjust page styling (2eec5c9)


0.3.5 (2020-08-08)


BUG FIXES

 * fix type error (f6cdad5)


0.3.4 (2020-08-07)


FEATURES

 * add node counts for every filter value and badge (67c7cba)


0.3.3 (2020-08-06)


BUG FIXES

 * add missing color value in colorings (116db0e)
 * ensure "Unknown" category is listed first (67e100c)
 * fix incorrect import (56e1274)
 * fix type error (1b07220)
 * lint (5c9eab4)
 * lint (1301184)
 * rename variable to clarify the intent (d318594)


FEATURES

 * add a foot note about the "Unknown" regions (1d35ed2)
 * add button to clear filters (d7de823)
 * add clade and QC status tree filters (2ca357c)
 * add clear button, disable autocomplete and spell check (7e2c319)
 * add colorings for "Unknown" regions (abd366b)
 * add filtering actions (3b5aa7b)
 * add node type tree filter (bb35c35)
 * add region tree filters (d2a809e)
 * add version number in the main title (cbb5518)
 * allow to remove filters by clicking a button on the badge (6bed38a)
 * allow to search for filtering criteria (61b5a25)
 * assign new nodes to the "Unknown" region (a04e0d5)
 * disable clear filter button when there are no filters to clear (4fbc5da)
 * display badges for filtering criteria (a1b70ed)
 * improve sizing and spacing of the filter panel elements (c682c78)
 * make filtering badges bigger and brighter (3cf8f5b)
 * make order of filtering criteria consistent (94ad967)
 * match background color with auspice sidebar (68be816)
 * prettify filtering badges (74f8714)
 * reduce margin (4b12a75)
 * rename unknown value back to "Unknown " (e6ce061)


0.3.1 (2020-07-30)


BUG FIXES

 * add missing env vars for vercel (62eaa01)
 * automate auspice monkey-patching (d27a9c5)
 * avoid incorrect absolute imports (66dcb4d)
 * avoid redux error about non-existing query auspice reducer (d6c141f)
 * disable debug console messages for i18next (56baa17)
 * don't call clade match if position isn't covered by the alignment (045984f)
 * ensure absolute URLs in the SEO tags (88c1615)
 * ensure auspice tooltips are not empty (c3f0ab3)
 * ensure translations are loaded properly (7bca9de)
 * ensure vercel url has https schema (462a76f)
 * ensure vercel url has https schema (f1462f6)
 * ensure zero positions don't trigger errors (fda012e)
 * fix incorrect seo tag name (8059e39)
 * fix object merging (50e1761)
 * format (638ee3a)
 * implement babel caller check as described in docs (2cc4e5a)
 * lint (a04cb05)
 * lint (25393fa)
 * lint (640a6d5)
 * lint (074d4ed)
 * lint, fix type errors, cleanup (e9ac5a0)
 * make parser robust to various line delimiters and unexpected characters
   (7c000b2)
 * make sure locateInTree() is reentrant (3bd0698)
 * patch auspice to remove more references to window (8a50144)
 * remove erroneous env var (8541468)
 * remove spaces in env files (7d79926)
 * remove unsupported syntax from babel config (7fdb15f)
 * show sequences being analyzed again (04b501c)


FEATURES

 * add "powered by auspice" logo on tree page (294a2c2)
 * add auspice reducers (6482351)
 * add auspice sidebar (71e1f56)
 * add button to show auspice tree (234f5e5)
 * add google meta tags (7cf4f63)
 * add help tips for results table column (0257e44)
 * add more data to tree node popup (0e69173)
 * add more meta tags for og and twitter (0dc4f43)
 * add padding for top panel (94b9d60)
 * add QC flags to the tree node popups (5aed898)
 * add redux thunk (b74a1a2)
 * add redux-logger (c2d7992)
 * add styled-components theme (8d29882)
 * add styled-components theme from auspice (5ec57d1)
 * add twitter and facebook meta tags (f5fca2a)
 * adjust legend's margin (f71cc7b)
 * allow loading fake auspice state for development (72733ad)
 * attach new nodes to reference nodes only (6dc7321)
 * autosize the tree (2e1aad5)
 * color tree nodes explicitly by QC status and type (5a1f976)
 * disable tree button until the analysis is done (b09492e)
 * display aminoacid mutations in auspice tree (811ea79)
 * import and build auspice as a part of webpack build (9d75bae)
 * improve visibility of nodes in QC coloring (3ecd30f)
 * improve webmanifest (3a6045e)
 * include auspice translation bundles (03791e8)
 * integrate auspice json generation into UI (17d920c)
 * make closes nodes brighter, shorten node type text (4deb988)
 * make help buttons larger (504a63a)
 * make tree button more visible (4f51b2a)
 * mark constants as const (6ead3e5)
 * move SEO tags into separate component, use react-helmet (b220e97)
 * move some of the SEO tags to _document, for static rendering (a35c820)
 * pass domain name to the client side (9624955)
 * port locate_in_tree.py to typescript (7c6c164)
 * prerender styled-components stylesheets (d88a9cf)
 * prettify tree page (e5a241e)
 * prettify tree page and related components (e8a15d9)
 * put custom coloring at the top of the dropdown list (c1ed74b)
 * reduce sidebar top spacing (94fc062)
 * remove coloring of closest nodes on the tree (fa5424e)
 * remove unused date and dataset choice widgets from auspice sidebar (3235278)
 * remove unused getInitialProps to allow static prerendering (df30618)
 * render auspice tree (fb2513f)
 * use nexstrain logo spinner for loading page (db21817)


0.2.2 (2020-07-17)


BUG FIXES

 * remove console warning (23850fe)


0.2.1 (2020-07-17)


BUG FIXES

 * adjust styling for breaking changes in react-file-icon v3 (902f045)
 * bring back regenerator-runtime in workers (eec18b2)
 * ensure filtered results are updated when results are updated (39d6601)
 * fix negative width in svg viewbox (b32a4f6)
 * format (9727f63)
 * hide filtering panel by default (0991119)
 * lint (5f0c2a1)
 * lint (d9e8707)
 * lint (fa6242a)
 * lint (28020ea)
 * make parser robust to various line delimiters and unexpected characters
   (afbcfd6)
 * make sure gene map tooltip appears reliably (19ec421)
 * make sure the icon in dev alert is not overlapped by text (5755956)
 * only match the last clade in the array of clades when filtering (0a3c0ad)
 * packages/web/package.json & packages/web/yarn.lock to reduce vulnerabilities
   (17c1e2b)
 * prevent sequence text from wrapping (1117cf3)
 * prevent vertical scrolling of navbar (32fb39d)
 * remove unnecessary core-js import from workers (bd9ec93)
 * reverse sort order (75fd269)
 * sort only sequences that makes sense to sort (ccd6daf)
 * typos (fc80cc2)


FEATURES

 * add basic virtualization to the table (b2e2d11)
 * add filter dialog popups (124ffe3)
 * add filtering by presence of QC issues and errors (712de18)
 * add filtering by aminoacid changes - gene, ref, position, query (77bbedf)
 * add filtering by aminoacid mutations (3b7759f)
 * add filtering by clade (6ee0b3b)
 * add filtering by nucleotide mutations (98f2d4b)
 * add filtering by sequence name (62cc172)
 * add flexbox fixes for internet explorer (e604b04)
 * add id column to results table (ea0994c)
 * add logos (f25e511)
 * add more mutation syntax options (937ac73)
 * add mutation parser (8e88955)
 * add polyfils (add5dd6)
 * add sort by sequence name (6f8721c)
 * add sorting for all categories (5a2efc5)
 * add table border (2e796ab)
 * add table border and shadow for when rows don't fill the area (73e092e)
 * add transpiled modules whitelist (115cdb1)
 * adjust filter button style - layout, position, margins (fa09ed5)
 * adjust gene map width (4db941b)
 * adjust sort and filter buttons sizes and positions (39f4e19)
 * adjust table column widths to accommodate filter and sort buttons (85551b9)
 * avoid main title text overflow (99b621b)
 * bring back the genome map (0513fa6)
 * bring back the genome map axis (fdeedfb)
 * bring back the old layout for the main page (756d496)
 * bring back the results status panel (a92114d)
 * constrain main page container width (727aad0)
 * don't go to /results page (2225bb4)
 * enforce horizontal scrolling on results page if the screen is to narrow
   (3e2e409)
 * ensure columns are of correct and equal width, prettify (e169137)
 * increase sequence name column width (a99e15b)
 * increase sequence name column width to 300px (f8b53eb)
 * make feature boxes responsive (8780343)
 * make filter panel collapsible, prettify its contents (d6714c2)
 * make footer prettier (ae8a4d8)
 * make footer responsive (c1644b9)
 * make pending rows dimmer and of the same color (fbcfcac)
 * polyfill CSS.escape for internet explorer (c120f8a)
 * prettify filter panel (b40dcf0)
 * reduce margins, text sizes on small screens, prevent overflow (160459c)
 * reduce minimal width to fit on iPad, adjust padding (e7b666a)
 * remove filter buttons in column headers (1d21fa3)
 * sort errored sequences as the ones with the worst QC result (90599d2)
 * trim filter strings, allow more delimiters (26182d1)
 * dev: add flag to allow setting fake data and navigating to results page
   (b618735)


0.1.2 (2020-07-03)


BUG FIXES

 * avoid crash in export when there are failing sequences (6e65d77)
 * enable export button even if some of the sequences fail (dd60ed9)
 * lint (90dbbb7)
 * remove fake entries (145b61a)


FEATURES

 * add basic analysis failure reporting (27736ba)


0.1.1 (2020-07-02)


BUG FIXES

 * add missing hook dependency (1f0de52)
 * allow indexing of the website (92e10c9)
 * apply eslint autofixes (488cae3)
 * avoid html validation errors (d5627b2)
 * break dependency cycles (4700de2)
 * clarify that the tooltip currently shows all the clades (ac12ea6)
 * display positions as 1-based (4940513)
 * display positions as 1-based for real (bc31c28)
 * don't shift svg rectangles by half-width (481359b)
 * ensure aminoacid changes are shown correctly (79453b8)
 * ensure isSequenceInClade is typed (3fe6fcb)
 * ensure type checks can be enabled (0644baf)
 * ensure typing of raw imports (499a5d7)
 * fix deepscan issues (ebaa8f6)
 * fix guard condition in aminoAcidChange() (1d9df44)
 * fix guard condition in aminoAcidChange() (978a9f6)
 * fix implicit use of React (465a082)
 * fix imports (f5af2aa)
 * fix lint and type errors (8a9d7a3)
 * fix tests for nucleotide range retrieval (4991506)
 * fix type mismatch (4fe0a1a)
 * fix typings (f780257)
 * grammar (1d948c1)
 * improve button styles (532c93e)
 * improve translations (95cf881)
 * lint (8d85353)
 * lint (be874ae)
 * lint (af82d9f)
 * lint (c36c6a9)
 * lint (da9c98d)
 * lint (4eb882c)
 * lint (6567a4b)
 * lint (0eaa7c9)
 * lint (c79c2ca)
 * lint (f95d453)
 * lint errors (6309298)
 * lint errors (cbf9215)
 * lint errors (404bbf7)
 * lint errors (add6b26)
 * lint errors (9047a0a)
 * make "back" button to actually go back, not to a specific page (9cd3c91)
 * make sure "dirty" flag is set properly (4f4024d)
 * make sure "to results" button shows up (05b77d0)
 * make sure settings saga is being run (28095a8)
 * packages/web/package.json, packages/web/yarn.lock & packages/web/.snyk to
   reduce vulnerabilities (73555b8)
 * packages/web/package.json, packages/web/yarn.lock & packages/web/.snyk to
   reduce vulnerabilities (d1ab37a)
 * remove aligned query from results (0a3f999)
 * remove redundant table borders (25c016d)
 * remove unused and vulnerable packages (9214419)
 * rename file to clarify intent (2b6a213)
 * resolve Threads.js workers bundling error in production (bd775a8)
 * silence eslint rule that produces false positives in typescript (c3b0e48)
 * silence more new eslint rules that produce false positives in typescript
   (a76cf14)
 * soften border color (763e227)
 * trim whitespace and line ending characters from reference sequence (86cd548)
 * type and refactor getAllAminoAcidChanges (1e95f2f)
 * type errors (92486a7)
 * type errors in saga (fefdace)
 * dev: disable eslint cache for consistent results, disable checker profiling
   (3f9962e)
 * dev: ensure webpack watches the typings (f0a667d)
 * dev: make sure type checking can be disabled (5f4918b)


FEATURES

 * add "to results" buttons on main page, prettify "back" button (887ca23)
 * add aminoacid changes to sequence name tooltip (4b7b232)
 * add aminoacid mutations to mutation tooltips (5643863)
 * add back and settings buttons (ff6f359)
 * add basic progress indicator (1ac9736)
 * add basic SEO tags (5e597df)
 * add basic sequence visualization (d2bd0cb)
 * add beta badge (97bcf43)
 * add clade info to the tooltips (5588cd1)
 * add clade marks to gene map (b197d3b)
 * add csv export (59247dc)
 * add exports to both JSON and CSV using dropdown button (47e8570)
 * add favicons (0ff52c7)
 * add footer branding (4ae2d37)
 * add French to language selector (04c7f4c)
 * add gene map (e938c68)
 * add list of non-ATTGCN to tooltips (bbe2a61)
 * add more languages (15dd09c)
 * add mutation tooltips (f2bfc64)
 * add navigation bar, routing and about page (7bc2fff)
 * add Ns and Gaps to the table (d443df6)
 * add numbered X axis (position) to sequence view (6d6304a)
 * add progress bar embedded into the drop box (2d058a6)
 * add proper results table (1bd4a49)
 * add results download (840aa80)
 * add tooltips for the "sequence" and "clades" columns (55e1cbe)
 * add total number of mutations to the table (04352f0)
 * add tree of clades (4baa357)
 * add upload (a4c0bde)
 * add version text to footer (ee74087)
 * allow parameters for multiple viruses (4295cf6)
 * avoid opening input box to speedup navigation to results page (5d87ca8)
 * borrow some more styling and components from nextstrain.org (d264601)
 * change example link text (bb99908)
 * change nucleotide colors (fb22e96)
 * change text for clade mutations (aff5073)
 * cleanup and simplify marker tooltips (34e54f9)
 * cleanup gene tooltip (87ec1ef)
 * disable export button until the processing is complete (1d50eb4)
 * display alignment score (fb62658)
 * don't wrap the text in text area (a8824b4)
 * filter out empty clades (f7405c0)
 * format mutations (c49a5e2)
 * format totals and clades in tooltips (4361528)
 * group clades in mutation tooltips on gene map (6971f9c)
 * implement reducer for updating results (cae5fb1)
 * improve sequence view styling in dark mode (b0e1327)
 * improve styling (8d1fe93)
 * limit number of mutations in the tooltip to 10 (4d6f077)
 * load example data when clicking the link (7ceeed9)
 * load no data, avoid running on startup (fec2219)
 * make it more like nextstrain (44092d7)
 * make layout container fluid (551a958)
 * make separate runs per sequence in a saga (662b3b8)
 * make sure eslint, tsc and stylelint can be disabled in production (d3c5f29)
 * make sure redux dev tools can be enabled in production (4cb3622)
 * make upload zone flat (5ccf82c)
 * mention freedom and openness, add todos for more content (5b1dcec)
 * move file reader into parser worker (5837c05)
 * navigate to results page on input change (538d6e2)
 * persist input box state on navigation (52aa653)
 * prefetch index and results page for instant navigation (8f3716d)
 * prettify dev alert (b6c1795)
 * prettify feature boxes (641183c)
 * prettify hero section on landing page (a99a792)
 * prettify info section (95302ba)
 * prettify mdx content (ae52e18)
 * reduce text spacing the the tooltip (1c7176f)
 * reimplement the old behavior in react (fec0942)
 * remove "Results" nav link (010f6f9)
 * remove About page (8ba236a)
 * remove input's border to not conflict with card border (92cd724)
 * remove percentage text from the progress bar (05d2623)
 * render results from Redux store (de2d75a)
 * reorganize the About section (2df61f8)
 * replace QC text with icons (56be063)
 * reset all translations (766977f)
 * restrict container size to lg (24145db)
 * retrieve input text back from reader/parser worker (c75ea79)
 * run sequence analysis in a worker pool concurrently (per sequence) (a96f138)
 * run the algorithm in a webworker (54fcbee)
 * run, navigate to results, and open paste dialog only when dropped a file
   (b3b7472)
 * set gene colors from auspice (5d90436)
 * setup production build and static compression (7cb0fac)
 * show all clades (c598f7b)
 * show and focus input box, delay paste when loading the example (7f5dbcc)
 * show sequence names early on, before analysis is completed (a5d8754)
 * show the gaps and Ns on the plot (0704fb2)
 * show uploaded file name and size on the drop area (039a0c5)
 * split upload and results into separate pages (862ca3d)
 * translate more strings (37dd6db)
 * write input filename and size into state (61f1591)


0.1.0 (2020-06-11)

Development started

switch-check
switch-x

Show when a new version is available
OK