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