Fastq_quality_filter allows to filters sequences based on quality score. You need to specify both the minimum accepted quality and the minimum percent of bases that must meet this quality score per read. Fastq files can be used
Parent program: fastx_toolkit
FASTX-Toolkit is a software package for preprocessing output data produced by Next-Generation sequencing machines in FASTA and FASTQ format before the main processing (assembling, mapping etc.). FASTQ to FASTA conversion, statistics calculation, file customization, quality-based preprocessing, trimming and etc. can be provided.