Cutadapt 

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. The program was initially developed to trim 454 sequencing data collected by Zeschnigk et al. As insertions and deletions within homopolymer runs are common in 454 data, cutadapt supports gapped alignment. For small RNA data analysis by Schulte et al., the program was modified to support trimming of colour-space reads. It has also been tested and works well on Illumina data. Cutadapt can search for multiple adapters in a single run of the program and will remove the best matching one. It can optionally search and remove an adapter multiple times, which is useful when (perhaps accidentally) library preparation has led to an adapter being appended multiple times. It can either trim or discard reads in which an adapter occurs. Reads that are outside a specified length range after trimming can also be discarded. To decrease the number of random hits, a minimum overlap between the read and adapter can be specified. In addition to adapter trimming, low-quality ends of reads can be trimmed using the same algorithm as BWA. (http://code.google.com/p/cutadapt/ )