Vibrio spp sub-workflow for TheiaProk

theiagen / public_health_bacterial_genomics

GNU Affero General Public License v3.0

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Open emmadoughty opened 2 years ago

emmadoughty commented 2 years ago

Identification of genes of interest using GeneFinder (https://github.com/phe-bioinformatics/gene_finder). Genes of interest available via VFDB for Vibrio (http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=Vibrio) and curated taxa-specific list (ask Emma).

Unfortunately GeneFinder is not available in Docker already

kapsakcj commented 1 year ago

will be addressed via PR #216 , at least for Vibrio cholerae. Not sure if there are tools specific to other Vibrio species or not

sage-wright commented 1 year ago

resolved in PHB and #216