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Vibrio spp sub-workflow for TheiaProk #139

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emmadoughty opened this issue Aug 24, 2022 · 2 comments
Open

Vibrio spp sub-workflow for TheiaProk #139

emmadoughty opened this issue Aug 24, 2022 · 2 comments
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enhancement New feature or request priority:1 (low) lowest priority. On the back burner

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@emmadoughty
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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
@emmadoughty emmadoughty added enhancement New feature or request priority:3 (medium) normal priority/urgency labels Aug 24, 2022
@emmadoughty emmadoughty added priority:1 (low) lowest priority. On the back burner and removed priority:3 (medium) normal priority/urgency labels Dec 7, 2022
@kapsakcj
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kapsakcj commented Apr 6, 2023

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
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resolved in PHB and #216

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@kapsakcj @sage-wright @emmadoughty