3.15.0

3.15.0

Nextclade Web: fix country colorings in output tree json #1646

Colors for "country", "region" and "division" are now correctly displayed in tree view

CDS coverage #1514

Nextclade now calculates amino acid coverage of each CDS. You can find this information:

• in output files: in the column or field cdsCoverage
• in Nextclade Web: in the tooltip of the "Cov." column on "Results" page

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. ⌨️ Source code is on GitHub: github.com/nextstrain/nextclade 🚩 Report bugs, suggest features by submitting a GitHub issue 💾 Nextclade datasets are here

3.14.5

3.14.5

Nextclade Web: disable "Relative to" dropdown when dataset has no reference tree

When using a dataset without reference tree for analysis, the "Relative to" dropdown has no meaning - the target for comparisons is always reference sequence node, because there is no information about any other nodes. We now disable this dropdown for datasets without trees.

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. ⌨️ Source code is on GitHub: github.com/nextstrain/nextclade 🚩 Report bugs, suggest features by submitting a GitHub issue 💾 Nextclade datasets are here

3.14.4

3.14.4

Fix seed coverage calculation for short references

During alignment, seed coverage is now computed as the total seed length divided by the shorter of the query or reference. This ensures correct behavior when references are shorter than queries, without requiring artificially low min_seed_cover values.

Nextclade Web: fix crash when using ?multi-dataset URL parameter

When used ?multi-dataset URL parameter, Nextclade Web could crash under certain conditions. This has been fixed.

Nextclade Web: workaround double run

When using URL parameters, Nextclade could sometimes spawn multiple copies of the analysis run. This could result in duplicated sequences being reported in the results table erroneously as well as in other unwanted effects. We added a workaround to mitigate this problem. Please report bugs by submitting a GitHub issue.

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. ⌨️ Source code is on GitHub: github.com/nextstrain/nextclade 🚩 Report bugs, suggest features by submitting a GitHub issue 💾 Nextclade datasets are here

3.14.3

3.14.3

Fix dataset suggestions and sorting for short references

Update minimizer-based scoring to better handle cases where the reference sequence is much shorter than the query sequence. The previous approach assumed full-genome references and could underestimate scores for partial references such as single genes. The revised method adjusts the normalization to avoid penalizing such cases, improving robustness without requiring changes to the index format. This resolves issues observed in datasets like yellow fever.

This improves dataset suggestions in Nextclade Web and dataset detection in nextclade sort CLI command. This also changes the scale of values of column score in the TSV output of nextclade sort command.

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. ⌨️ Source code is on GitHub: github.com/nextstrain/nextclade 🚩 Report bugs, suggest features by submitting a GitHub issue 💾 Nextclade datasets are here

3.14.2

3.14.2

Nextclade Web: crash with custom Auspice JSON dataset

When an Auspice JSON dataset is provided as whole-dataset input through ?dataset-json-url, Nextclade Web could crash under certain conditions. 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. ⌨️ Source code is on GitHub: github.com/nextstrain/nextclade 🚩 Report bugs, suggest features by submitting a GitHub issue 💾 Nextclade datasets are here

3.14.1

3.14.1

Nextclade Web: crash with custom datasets

When a custom dataset is provided through ?dataset-url, Nextclade Web could crash under certain conditions. This has been fixed. Issue PR

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. ⌨️ Source code is on GitHub: github.com/nextstrain/nextclade 🚩 Report bugs, suggest features by submitting a GitHub issue 💾 Nextclade datasets are here

3.14.0

3.14.0

Nextclade Web: multi-dataset mode

Nextclade Web now allows to run analysis for multiple datasets at once.

You could provide sequences belonging to multiple organisms or for the same organism, but based on different reference sequences. On "Multiple datasets" tab, Nextclade will try to deduce datasets that are best matching your sequences. You can then proceed to running analysis for each dataset. If multiple datasets have been detected, you will see a "Dataset" dropdown on "Results", "Tree" and "Export" page, which allows you to switch between results for different datasets.

In multi-dataset mode, the "Export" page now also contains an "Export all to Excel" button, which allows to download .xlsx file containing all analysis results in tabular format, one dataset per sheet. This is the same data as in CSV/TSV files, but aggregated into a single file.

When starting Nextclade analysis using URL parameters, you can add ?multi-dataset to run in multi-dataset mode.

Nextclade is now using new global search algorithm to find the suggested datasets for your sequences. It tries to minimize the number of datasets, while optimizing their relevance.

This is a convenience feature, i.e. the analysis runs for each dataset are still independent, just like in single-dataset mode, except you don't need to run multiple analyses for each dataset manually now.

This could be useful if you analyze one or multiple a FASTA files containing a mixture of sequences obtained from different organisms, strains or genome segments.

Nextclade Web: add "Download SVG" button to "Tree" page

There is now a "Download SVG" button in the top-right corner of the "Tree" page. It allows to download the tree visualization and other contents of the page, including applied filters and zoom, to an SVG file. This functionality is similar to that is offered by Auspice.

Nextclade Web: add "Focus on selected" toggle on "Tree" page

Adds a sidebar toggle on "Tree" page that emphasizes visible nodes by expanding them to occupy more vertical space, improving focus on filtered or zoomed subsets. Designed to enhance visibility in large phylogenetic trees. This is an Auspice feature which was introduced in Auspice 2.59.0 and now also available in Nextclade.

Nextclade CLI: global dataset search mode for sort command

You can now add --global to sort command to enable global search algorithm to find the minimal set of suggested datasets for your sequences. Note that this mode disables streaming of results, because the optimization step requires knowing datasets for all sequences in advance. This may lead to increased memory consumption for large inputs.

This is an experimental feature. Use with caution.

Nextclade CLI: fix panics

Some of the expected errors (e.g. invalid input files) in Nextclade CLI would previously cause panics (crashes). Now these errors are handled more gracefully and the visual output of these errors to the console is now cleaner and more concise.

Nextclade CLI: fix console color mode handling

Nextclade CLI previously output colored messages (with ANSI sequences) even if output is not a TTY (e.g. redirected to a file). This has now been fixed.

For additional configuration, the CLI arguments have been added, as well as proper handling of environment variables typically used to control console coloring.

The following priority rules apply:

• Nextclade detects output target (TTY or not) and outputs appropriately for the target by default

• If any of the environment variables: COLOR (auto|always|never), NO_COLOR (set), CLICOLOR_FORCE=1 are found, then they override the default

• If arguments --color=auto|always|never or --no-color (shortcut for --color=never) are found, they override the defaults and environment variables. If multiple --color or --no-color arguments present, then only the argument that comes last is taken into account.

Known issue: --help coloring is not affected by --color and --no-color arguments: #1629

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. ⌨️ Source code is on GitHub: github.com/nextstrain/nextclade 🚩 Report bugs, suggest features by submitting a GitHub issue 💾 Nextclade datasets are here

3.13.3

3.13.3

Fix crash when exporting annotations for sequences with missing genes

Nextclade Web and CLI would crash when attempting to output GFF and TBL files where entire genes are unsequenced or otherwise missing. 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. ⌨️ Source code is on GitHub: github.com/nextstrain/nextclade 🚩 Report bugs, suggest features by submitting a GitHub issue 💾 Nextclade datasets are here

3.13.2

3.13.2

Speed up Nextclade web, fix crash when using files >45MB on Chromium v136 browsers

In recently releaed version 136, Chromium-based browsers (e.g. Chrome, Edge) reduced the maximum allowed fixed array size, causing Nextclade web to crash when files bigger than 46,505,915 bytes are used.

It turns out that avoiding the need for a large array gets rid of most of the delay between clicking "Run" and the start of the analysis. For files of ~60MB the time saved is on the order of 5 seconds. A small but noticeable performance win! See issue #1605 and PR #1606 for more details.

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. ⌨️ Source code is on GitHub: github.com/nextstrain/nextclade 🚩 Report bugs, suggest features by submitting a GitHub issue 💾 Nextclade datasets are here

3.13.1

3.13.1

Fix crash on empty query annotations

For certain samples which end up with an empty output genome annotation Nextclade Web could crash. This is now resolved.
See #1601,#1602. Thanks @theosanderson for reporting.

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. ⌨️ Source code is on GitHub: github.com/nextstrain/nextclade 🚩 Report bugs, suggest features by submitting a GitHub issue 💾 Nextclade datasets are here