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geNomad v1.7.0
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@apcamargo apcamargo released this 14 Sep 00:22
· 41 commits to main since this release
v1.7.0
4f18ff8

Changed

  • The mmseqs search command has been replaced by a two-step alignment workflow. In the first alignment step, --alignment-mode 1 and --max-rejected are utilized, while the second step uses --alignment-mode 2 and -c 0.2. This change reduces the number of alignments that are rejected due to not meeting the minimum coverage cutoff and mitigates the issue where the annotation results change when the input sequence order is altered.
  • The --min-ungapped-score parameter of mmseqs prefilter was increased from 20 to 25.
  • The --max-rejected parameter of the first mmseqs align step was increased from 225 to 280.
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