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.
To run this software in a Linux environment run the commands:
module load cutadapt cutadapt
More details could be found at software homepage: http://cutadapt.readthedocs.org/en/latest/guide.html