pyfastq_filter

Filter FASTQ Files.

Installation

pip3 install --user pyfastq_filter

Usage

Usage:
  pyfastq_filter.py [-q i] [-l n] [-m m] [-o OUTNAME] FASTQ

Options:
  -l --length=n      minimum length to let through [default: 300]
  -m --max-length=m  maximum length to let through [default: infinity]
  -q --quality=i     minimum quality to let through [default: 10]
  -o --outfile=FILE  output filename, otherwise STDOUT [default: -]

Extract only FASTQ entries with sequence length >= 5000 and mean quality >= 12:

pyfastq_filter.py -q 12 -l 5000 example.fastq > example-q12-l5000.fastq