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@nextstrain-bot nextstrain-bot released this 04 Jun 16:49
3.7.0
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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.
Assets 9
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