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SWittouck / SCARAP

A toolkit for prokaryotic comparative genomics
GNU General Public License v3.0
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Core pipeline: write database with final selection of core orthogroups #8

Closed SWittouck closed 2 years ago

SWittouck commented 4 years ago

Currently, the core-pipeline command does not write a profile HMM database with the core orthogroups that were selected based on their presence in the full genome database (the "final" core orthogroups). The only profile HMM database that is written is the one with "candidate core genes" (= soft core genes in the seed genomes), created by the "build" step.

SWittouck commented 2 years ago

Fixed by commit da5dd35; the alignments and cutoffs of candidate single-copy core orthogroups that didn't make the final selection are now removed.