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Published November 15, 2022 | Version v1.2.0
Software Open

apcamargo/genomad: geNomad v1.2.0

Authors/Creators

  • 1. DOE Joint Genome Institute

Description

Changed
  • Mention the Zenodo upload of geNomad's database in README.md.
  • Add the following sentence for the help dialogue of the --min-plasmid-marker-enrichment, --min-virus-marker-enrichment, --min-plasmid-hallmarks, and --min-virus-hallmarks parameters: "This option will be ignored if the annotation module was not executed".
  • Apply a uniform prior to the empirical sample composition in score_batch_correction. This will shrink the effect of calibration when the empirical composition distribution is very skewed.
  • Reduce the --min-score in the README.md example to 0.7.
Fixed
  • Fix a bug in the score calibration module where the sample size was set to a constant value and the "Your sample has less than 1,000 sequences…" warning would always appear.

Files

apcamargo/genomad-v1.2.0.zip

Files (26.6 MB)

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Additional details

Related works

Is supplement to
https://github.com/apcamargo/genomad/tree/v1.2.0 (URL)