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Published January 31, 2023 | Version 2.11.0
Software Open

nextstrain/nextclade: 2.11.0

Authors/Creators

  • 1. Biozentrum, University of Basel
  • 2. @neherlab @nextstrain
  • 3. @FredHutch / @blab / @nextstrain
  • 4. @nextstrain
  • 5. @Snyk
  • 6. University of North Carolina
  • 7. University of Freiburg
  • 8. ETH Zurich @cevo-public
  • 9. Oklahoma Medical Research Foundation
  • 10. Faculty of Computer Science, Dalhousie University
  • 11. The Francis Crick Institute
  • 12. Fred Hutchinson

Description

Nextclade Web 2.11.0, Nextclade CLI 2.11.0 (2023-01-31) IMPORTANT: ensure index column is written to CSV/TSV output files in case of error

The new column index was correctly written when analysis of a sample succeeds. However, for analyses which ended up with an error (e.g. "Unable to align") this column was mistakenly missing. In this version we fix this omission.

Fix gene map width in Nextclade Web

Gene map (genome annotation) was misaligned with sequence views (not matching their width). This has been fixed in this version.

Add table row indices to results table in Nextclade Web

We added a column with index of the row in the table. This is useful for visual search and counting of sorted and filtered results.

Not to be confused with sequence index. Row indices always start with 0 and sorted in ascending order, and do not change their position when sorting or filtering the results.

These indices are not a part of output files. Nextclade CLI is not affected.

Improve error messages

Errors due to failure of sequence alignment are reworded and hopefully are more complete and comprehensible now. Additionally, we improved error message when reference sequence fails to read.

Always show action buttons on results page in Nextclade Web

On smaller screens the "Download", "Tree" and other action buttons were not visible by default and horizontal scrolling were required to see them. We changed the layout such that the panel with buttons does not overflow along with table and so the buttons are always visible. Table is still scrollable.

Improve wording on main page of Nextclade Web

We improved text on main page as well as descriptions inside HTML markup, adding more concrete information and keywords. This should be more pleasant to read and might improve Nextclade ranking in search engines.

<details> <summary><h3>Commit history</h3> (click to expand)</summary>

</details> Instructions

📥 Nextclade CLI & Nextalign CLI can be downloaded from the links in the "Assets" section just below. There click "Show all" to show more options. Note the difference between "nextalign" and "nextclade" files.

🌐 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

Files

nextstrain/nextclade-2.11.0.zip

Files (9.8 MB)

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md5:6f8f7686f3c29c819919329144b5cc43
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Additional details

Related works

Is supplement to
https://github.com/nextstrain/nextclade/tree/2.11.0 (URL)