cutadapt removes adapter sequences from high-throughput sequencing data. This is usually necessary when the read length of the sequencing machine is longer than the molecule that is sequenced, for example when sequencing microRNAs.
cutadapt was developed by Marcel Martin. cutadapt website.
helix% module load cutadapt helix% cd /data/user/mydir helix% cutadapt -a AACCGGTT input.fastq > output.fastq