nextstrain/nextclade: 3.0.1

NEXT

CLI

Bug fixes

• Fixed a bug introduced in v3.0.0 which caused the default path for translations to be incorrect. This affected only users who used --output-all without passing a custom path template via --output-translations. The new default path is nextclade.cds_translation.{cds}.fasta where {cds} gets replaced with the name of the CDS, e.g. nextclade.cds_translation.S.fasta for SARS-CoV-2's spike protein.

• Fixed a bug where nextclade dataset get command fails to download a dataset if a dataset has more than one version released.

Documentation

• Added a section to the v3 migration guide about the renamed default path for translations, a breaking change. The new default output path for translations is nextclade.cds_translation.{cds}.fasta. Before v3, the default path was nextclade_gene_{gene}.translation.fasta. You can emulate the old (default) behavior by passing --output-translations="nextclade_gene_{cds}.translation.fasta" to nextclade3.

Instructions

📥 Nextclade CLI & Nextalign CLI can be downloaded from the links in the "Assets" section just below. Click "Show all" at the bottom of the "Assets" section to show more download options. Note the difference between "nextalign" and "nextclade" files as well as differences in operating systems and computer architectures.

🌐 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