filter fastq reads by quality score usage: fastq_quality_filter [-h] [-v] [-q N] [-p N] [-z] [-i INFILE] [-o OUTFILE] Part of FASTX Toolkit 0.0.14 by A. Gordon (assafgordon@gmail.com) fastq_quality_filter -q 20 -p 90 -i input_1.fastq -o input_1_quality_filter.fastq Share it