geNomad v1.8.0

Added

• Added the --min-number-genes parameter to the summary module. This parameter allows users to set the minimum number of genes a sequence must encode to be considered for classification as a plasmid or virus. The default value is 1. When --conservative is used, this parameter is set to 1. When --relaxed is used, this parameter is set to 0. This filter has no effect if the annotate module is not executed.

Changed

• Added a hyperlink to the official documentation in the help dialogue.
• The virus taxonomic lineage is presented using a fixed number of fields separated by semicolons (;). As a result, for genomes that could not be assigned to the family level (the most specific taxonomic rank), there will be trailing semicolons at the end of the lineage string.
• Do not apply the gene-based post-classification filters when the annotate module is not executed.
• Set the default value of --min-plasmid-marker-enrichment to 0.1.