qual_trim.py1

positional arguments:

FASTQ

including stdin or compressed file {zip,gz,tar,bz}

optional arguments:

-h, --help

show this help message and exit

-b BASE

ASCII-encoded quality offset, e.g. 33 or 64 (default: 33)

-p PROB

error probability cutoff (default: 0.1)

-q SCORE

quality score cutoff (default: '-p 0.1')

-l BP

minimum read length in bp (default: 16)

--illumina5

Illumina 1.5+ encoding marked with 'B'

--solexa

Solexa encoding