custom database

[bionesiacourse]

Hi Hariszaf. Can PEMA use a custom database to assign taxa. If yes what would be the format?. Thanks.Aji

[cpavloud]

Hi @bionesiacourse !
Yes, PEMA can use a custom reference database.
But you will need

a) to train the classifier that will do the taxonomy assignment (the CREST classifier if you have 16/18S rRNA/ITS data or the RDPClassifier if you have COI data) and

b) to create a "custom_ref_db" folder containing a sequence alignment file (with a .fasta extension) and a taxonomy file (with a .nds extension) (in the CREST case) or a sequence file (with a .fasta extension) and a taxonomy file (with a .tsv extension) (in the RDPClassifier case).