Fastq_quality_trimmer trims (cuts) sequences based on quality threshold. This tool will cut the sequences from the end if the quality of a base drops below the given threshold. Also, you have an option to disregard all reads shorter than specified by -l after trimming. This tools works with fastq files
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.