help:

--version

show program's version number and exit

-h, --help

show this help message and exit

subcommands:

Filtering operation

length

Filters reads by length.

missing

Filters reads by N or gap character count.

repeats

Filters reads by consecutive nucleotide repeats.

quality

Filters reads by quality score.

maskqual

Masks low quality positions.

trimqual

Trims sequences by quality score decay.

output files:

<command>-pass

reads passing filtering operation and modified accordingly, where <command> is the name of the filtering operation that was run.

<command>-fail

raw reads failing filtering criteria, where <command> is the name of the filtering operation.

output annotation fields:

None