3.7.0

Nextclade 3.7.0

Use Auspice JSON as a full dataset (experimental)

Nextclade can now optionally use Auspice datasets (in Auspice v2 JSON format) not only as reference trees, but also as self-contained full Nextclade datasets. Nextclade will take pathogen info, genome annotation, reference sequence, and, of course, reference tree from Auspice JSON. No other files are needed. This allows to use almost any Auspice dataset (e.g. from nextstrain.org) as Nextclade dataset.

• In Nextclade CLI, --input-dataset argument now also accepts a path to Auspice JSON file (in addition to accepting the usual paths to a dataset directory and zip archive)

• Nextclade Web now has a new URL parameter dataset-json-url, which accepts a URL to Auspice JSON file or even to a dataset URL on nextstrain.org

This feature is currently in experimental stage. For details and discussion see PR #1455.

Make reference tree branch attributes optional

Nextclade now accepts Auspice JSONs without .branch_attrs on tree nodes.

Allow index and seqName in column selection

Previously, Nextclade treated output CSV/TSV columns index and seqName as mandatory and they were always present in the output files. In this release they are made configurable. One can:

• in CLI: add or omit index and seqName values when using --output-columns-selection argument
• in Web: tick or untick checkboxes for index and seqName in "Column config" tab of "Export" page

Add dataset capabilities

The table in the nextclade dataset list command now displays an additional column "capabilities", which lists dataset capabilities, i.e. whether dataset contains information allowing clade assignment, QC, etc. The same information is available in JSON format (unstable) if you pass --json flag.

Installation and usage 📚 Documentation: docs.nextstrain.org/projects/nextclade 🌍 Nextclade Web: clades.nextstrain.org 🖥️ Nextclade CLI: 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. 🐋 Docker images are available on DockerHub 🐍 Conda package is available in bioconda channel.

3.6.0

Nextclade 3.6.0

Make reference tree node attribute clade_membership optional

Previously Nextclade required clade information to be always present in the input reference tree in the form of the .node_attrs.clade_membership field on each tree node. However, for certain datasets we might not have or need clade information. Making such datasets required workarounds, such as adding an empty string to the clade_membership field.

In this version we make clade_membership field optional. This allows to make datasets without clades. This is useful when working with organisms for which clades don't make sense or for which the nomenclature is not sufficiently established. This is also useful for dataset authors, who can now bootstrap simple datasets without clades first and then add clades and other features gradually later.

With this change, if clade_membership is not present in the dataset's reference tree nodes, then

• Clade assignment will not run

• Any clade-related functionality will not work

• Output JSON/NDJSON result entries will not contain clade field

• Clade column in output CSV/TSV will be empty

• Clade column in Nextclade Web will be empty

This change does not affect any other parts of the application. Notably, clade-like attributes (from .meta.extensions.nextclade.clade_node_attrs), if present, are still assigned and being written to the output as before.

Installation and usage 📚 Documentation: docs.nextstrain.org/projects/nextclade 🌍 Nextclade Web: clades.nextstrain.org 🖥️ Nextclade CLI: 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. 🐋 Docker images are available on DockerHub 🐍 Conda package is available in bioconda channel.

3.5.0

Nextclade 3.5.0

Algorithm

Detect loss of amino acid motifs correctly

Nextclade sometimes failed to detect a motif loss if that motif was the only one in its category. This is now fixed and users could observe changes in detected lost motifs. This affects datasets using aaMotifs property in their pathogen.json file, notably the flu datasets.

Nextclade Web

Ensure currently selected dataset is reloaded when it changes remotely

When dataset-url URL parameter is provided Nextclade Web would not update the dataset's pathogen.json file when remote dataset changes without changing its version. This is now fixed. It only affected users providing custom datasets using dataset-url URL parameter.

General

Upgrade Auspice

The Auspice tree rendering package has been updated from version 2.52.1 to version 2.53.0. See the list of changes here

Installation and usage 📚 Documentation: docs.nextstrain.org/projects/nextclade 🌍 Nextclade Web: clades.nextstrain.org 🖥️ Nextclade CLI: 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. 🐋 Docker images are available on DockerHub 🐍 Conda package is available in bioconda channel.

3.4.0

Nextclade 3.4.0

Nextclade Web

Remove redundant scrollbars in dataset names

In dataset selector, sometimes there were extra scrollbars displayed to the right of the dataset names. This has been fixed.

Select suggested dataset automatically when suggestion is triggered manually

When suggestion is triggered manually, using "Suggest" button on main page, Nextclade will now automatically select the best dataset as the current dataset. Previously this could only be done by clearing the current dataset first and then clicking "Suggest". When suggestion algorithm is triggered automatically, the behavior is unchanged - the dataset will not be selected.

Nextclade CLI

Don't read dataset's tree.json and genome_annotation.gff3 unless they are declared

Nextclade CLI will no longer read tree.json and genome_annotation.gff3 from the dataset, unless they are declared in the pathogen.json. These are optional files and we cannot assume their presence or filenames.

Warn user if input dataset contains extra files

Nextclade CLI will warn users when input datasets contains extra files which are not declared in the dataset's pathogen.json, or if there's extra declarations of files in the pathogen.json, but the files are not actually present in the dataset. This is mostly only useful to dataset authors for debugging issues in their datasets.

Add Bioconda Linux ARM build

We added one more build variant to Bioconda distribution channel - for Linux operating system on 64-bit ARM hardware architecture. It uses nextclade-aarch64-unknown-linux-gnu executable underneath. This can be useful if you prefer to manage Nextclade CLI installation on your Linux ARM machine or in a Docker ARM container with Conda package manager. However, because Nextclade CLI is a self-contained single-file executable, we still recommend direct downloads from GitHub Releases rather than Conda or other installation methods.

Installation and usage 📚 Documentation: docs.nextstrain.org/projects/nextclade 🌍 Nextclade Web: clades.nextstrain.org 🖥️ Nextclade CLI: 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. 🐋 Docker images are available on DockerHub 🐍 Conda package is available in bioconda channel.

3.3.1

Nextclade CLI 3.3.1

Fix crash when using --verbosity option

Nextclade was crashing with internal error when --verbosity option was present. This has been fixed.

Installation and usage 📚 Documentation: docs.nextstrain.org/projects/nextclade 🌍 Nextclade Web: clades.nextstrain.org 🖥️ Nextclade CLI: 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. 🐋 Docker images are available on DockerHub 🐍 Conda package is available in bioconda channel.

3.3.0

Nextclade 3.3.0

General

Allow FASTA files with leading newlines

Previously Nextclade would report an error "Expected character '>' at record start" when input FASTA file contained trailing newline or when it was empty. This was fixed.

Nextclade Web

Don't run dataset suggestion when navigating to "Datasets" page

Dataset suggestion will no longer run each time "Datasets" page is opened

Upgrade Auspice tree renderer from version 2.51.0 to 2.52.1

See changelog here

Installation and usage 📚 Documentation: docs.nextstrain.org/projects/nextclade 🌍 Nextclade Web: clades.nextstrain.org 🖥️ Nextclade CLI: 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. 🐋 Docker images are available on DockerHub 🐍 Conda package is available in bioconda channel.

3.2.1

Nextclade 3.2.1

Nextclade CLI

Fix "Dataset not found" error when using nextclade dataset get with --tag argument.

This fixes a bug in the dataset filtering logic causing "Dataset not found" error when even correct name and tag were requested using nextclade dataset get with --tag argument.

Installation and usage 📚 Documentation: docs.nextstrain.org/projects/nextclade 🌍 Nextclade Web: clades.nextstrain.org 🖥️ Nextclade CLI: 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. 🐋 Docker images are available on DockerHub 🐍 Conda package is available in bioconda channel.

3.2.0

Nextclade 3.2.0

General

Minimizer search algorithm configuration has been improved

Minimizer search algorithm used in dataset auto-suggestion in Nextclade Web as well as in sort command of Nextclade CLI.

The default value for minimum match score (--min-score) has been reduced from 0.3 to 0.1. The default value for minimum number of hits (--min-hits) required for a detection has been reduced from 10 to 5. This should allow to better handle more diverse viruses.

If there is a sufficiently large gap between dataset scores, the algorithm will now only consider the group of datasets before the gap. The gap size can be configured using --max-score-gap argument in Nextclade CLI. The default value is 0.2.

Additionally, in Nextclade CLI sort command the algorithm now chooses only the best matching dataset. In order to select all matching datasets, the --all-matches flag has been added.

Nextclade CLI

Sequence index in the output TSV file of the sort command

The TSV output of the sort command (requested with --output-results-tsv) now contains additional column: index. The cells under this column contain index of the corresponding input sequence in the FASTA file. These indices can be used in the downstream processing to reliably map input sequences to the output results. Sequence names alone can be unreliable because they are arbitrary strings which are not guaranteed to be unique.

Installation and usage 📚 Documentation: docs.nextstrain.org/projects/nextclade 🌍 Nextclade Web: clades.nextstrain.org 🖥️ Nextclade CLI: 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. 🐋 Docker images are available on DockerHub 🐍 Conda package is available in bioconda channel.

3.1.0

CLI

PCR primers are back in Nextclade CLI

Due to popular demand, we are bringing back --input-pcr-primers argument for Nextclade CLI, which accepts a path to primers.csv file. The feature works just like it did prior to release of Nextclade v3, except primers.csv is never read from a dataset - you always need to provide it separately. At the same time, we removed support for primers field from pathogen.json, because it was too difficult to make a correct JSON object and it would conflict with the primers provided with --input-pcr-primers.

Web

Fix results table stripes

Results table stripes are always alternating now, regardless of sorting and filtering applied. This is only a visual change and does not affect any functionality.

Installation and usage 📚 Documentation: docs.nextstrain.org/projects/nextclade 🌍 Nextclade Web: clades.nextstrain.org 🖥️ Nextclade CLI: 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. 🐋 Docker images are available on DockerHub 🐍 Conda package is available in bioconda channel.

3.0.1

CLI

Bug fixes

• Fixed a bug introduced in v3.0.0 which caused the default path for translations to be incorrect. This affected only users who used --output-all without passing a custom path template via --output-translations. The new default path is nextclade.cds_translation.{cds}.fasta where {cds} gets replaced with the name of the CDS, e.g. nextclade.cds_translation.S.fasta for SARS-CoV-2's spike protein.

• Fixed a bug where nextclade dataset get command fails to download a dataset if a dataset has more than one version released.

Documentation

• Added a section to the v3 migration guide about the renamed default path for translations, a breaking change. The new default output path for translations is nextclade.cds_translation.{cds}.fasta. Before v3, the default path was nextclade_gene_{gene}.translation.fasta. You can emulate the old (default) behavior by passing --output-translations="nextclade_gene_{cds}.translation.fasta" to nextclade3.

Instructions

📥 Nextclade CLI can be downloaded from the links in the "Assets" section just below. Note the difference in operating systems and computer architectures.

🌐 Nextclade Web is available at https://clades.nextstrain.org

🐋 Docker images are available at DockerHub

📚 To understand how it all works, make sure to read the Documentation