-r refd

reference database in FASTA format

-t taxonomy

taxonomy file with sequence IDs matching the reference database

-a queryA

FASTA file containing query sequences (single-ended or read 1)

-b queryB

FASTA file containing query sequences (read b, with matching IDs)

-x

Reverse-complement query A sequences (required if they are provided in the reverse sense)

-y

Reverse-complement query B sequences (required if they are provided in the reverse sense)

-i regex

regular expression used to select part of the fasta header to use as the sequence id. Default: "(\S+)"

-l file

text file containing sequence IDs to process, one per line

-d delimiter

delimiter separating the two reads when provided in a single file

-m tempdir

temporary directory. Will be removed on successful completion, but likely not if there is an error

-f

for sequences where only one read is available, fall back to single-ended classification. Default: drop these sequences

-g

for sequences where one read is overly generic, do not fall back to single-ended classification. Default: classify these sequences based on only the more specific read