Hi! I was wondering if we could use our own reference database for a specific species instead of the premade ones in the Dropbox for the mapping step? If we can, is there a way to know exactly what we would need for the pangenome.tsv file to make it ourselves since that is really the only file it seems like we would have to make. Thank you!
For custom pangenome generation you can use the PanPhlAn pangenome exporter.
You will only need the fasta files of the reference genomes you want to use. It will generate a folder similar to the one you can download from the database.