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Published July 31, 2023 | Version v1.6.0
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apcamargo/genomad: geNomad v1.6.0

Authors/Creators

  • 1. DOE Joint Genome Institute

Description

Changed
  • Update numba (>=0.57) and numpy (>=1.21) version requirements.
  • Use casefold for sequence comparison within the Sequence class.
  • Remove type annotations of methods of the Sequence class that return an instance of Sequence.
  • Use console.status to log the deletion of the .tar.gz file during the execution of download-database.
  • Make the conservative assignment at the family level optional via the --conservative-taxonomy parameter. This increases the amount of viral genomes assigned to a family when executing geNomad with default parameters.
Fixed
  • Fix parameter names in the error message of --conservative and --relaxed (e.g. --min_score → --min-score).

Files

apcamargo/genomad-v1.6.0.zip

Files (28.4 MB)

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md5:36338dcf28c23dcd6f7cc6aa35d8225f
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Additional details

Related works

Is supplement to
https://github.com/apcamargo/genomad/tree/v1.6.0 (URL)