help:

--version

show program's version number and exit

-h, --help

show this help message and exit

subcommands:

Alignment method

align

Find primer matches using pairwise local alignment.

score

Find primer matches by scoring primers at a fixed position.

extract

Remove and annotate a fixed sequence region.

output files:

mask-pass

processed reads with successful primer matches.

mask-fail

raw reads failing primer identification.

output annotation fields:

SEQORIENT

the orientation of the output sequence. Either F (input) or RC (reverse complement of input).

PRIMER

name of the best primer match.

BARCODE

the sequence preceding the primer match. Only output when the --barcode flag is specified.