nextstrain/nextclade: 3.8.0
Authors/Creators
- Ivan Aksamentov
- Richard Neher1
- Cornelius Roemer2
- mt-gitlocalize
- Anna (Anya) Parker
- Victor Lin3
- Daniel Antonio Negrón
- Nextstrain bot4
- John SJ Anderson5
- Thomas Sibley
- Snyk bot6
- Emma Hodcroft7
- Actat
- Alex Rubinsteyn8
- Björn Grüning9
- Bryan Tegomoh
- Chaoran Chen10
- Christopher Bottoms11
- Finlay Maguire12
- John Huddleston13
- Jover Lee
- Theo Sanderson14
- Elias Harkins
- 1. Biozentrum, University of Basel
- 2. @neherlab @nextstrain
- 3. @FredHutch / @blab / @nextstrain
- 4. @nextstrain
- 5. @nextstrain / @blab
- 6. @Snyk
- 7. @SwissTPH
- 8. University of North Carolina
- 9. University of Freiburg
- 10. ETH Zurich @cevo-public @GenSpectrum
- 11. Oklahoma Medical Research Foundation
- 12. Community Health & Epidemiology / Computer Science, Dalhousie University
- 13. @blab @nextstrain
- 14. The Francis Crick Institute
Description
Nextclade 3.8.0
Relative mutations
Nextclade now calls mutations relative to multiple targets. Additionally to previously available mutations relative to reference and mutations relative to parent tree node (private mutations), Nextclade now calls mutations relative to clade founder tree nodes, and relative to custom nodes of interest if defined in the dataset (e.g. vaccine strains).
Nextclade Web now has an additional dropdown selector for the target of mutation calling. Output files has new columns/fields for mutations relative to clade founders (founderMuts) as well as for mutations relative to custom nodes (relativeMutations).
See documentation for more details.
Update Auspice tree visualization to 2.56.0
Auspice tree visualization package has been updated from 2.55.0 to 2.56.0. See Auspice changelog here.
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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.
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Files
nextstrain/nextclade-3.8.0.zip
Files
(14.8 MB)
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md5:5ea6be4b9e28b6bb8f76f519c9714f4a
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Additional details
Related works
- Is supplement to
- Software: https://github.com/nextstrain/nextclade/tree/3.8.0 (URL)