This release of the pipeline can be run with the following biomes:
Other biomes can be supported under request by raising an issue in this repo.
Sourmash is the default tool to generate taxonomic profiles. Optionally, bwamem2 can be used as well.
Pangenome function tables are used by default to generate functional profiles. Core functions can be used as well.
Databases are downloaded using the bash script provided. MGnify hosts all DBs needed, so the user doesn't need to generate them from scratch.