Fastx_clipper removes sequencing adapters or linkers from the reads, can work both with fasta or fastq files. You can also specify whether you would like to keep sequences which contained adapters or which did not contain adapters. You can discard sequences shorter than N nucleotides
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.