Taxonomy

Jump to bottom Edit New page

Aaron edited this page Apr 9, 2019 · 1 revision

Generating a [GTDB/SILVA] to [SILVA/GTDB] summary file.

GTDB to SILVA: gtdb taxonomy gtdb_silva_export --output /tmp/gtdb_to_silva.tsv

SILVA to GTDB: gtdb taxonomy silva_gtdb_export --output /tmp/silva_to_gtdb.tsv

Prerequisites:

ConfigMetadata requires the GTDB_SSU_SILVA_MAPPING variable to be set to the current SILVA taxonomy file obtained from here
ConfigMetadata requires the GTDB_SSU_SILVA_AGGREGATE variables to be set, this is an aggregate of all SSU BLAST taxonomy files from each representative genome. This is generated by running scripts_dev/silva_aggregate_last_hits.py