Glossary of Terms

top-level directory - the highest, or first, folder, in which the pipeline lives. It's almost certainly called its_glue, unless you changed it. The pipeline must be run from inside this folder.

reference database - A fasta formatted file of sequences with taxonomic information in the headers. To be used to match query sequences (your sequences) against for the purposes of assigning taxonomy. Can be compressed, e.g. db.fasta.gzip.