Cutadapt: trim adapters from high-throughput sequencing reads

Cutadapt finds and removes adapter sequences, primers, poly-A tails
and other types of unwanted sequence from your high-throughput
sequencing reads.

Cleaning your data in this way is often required: Reads from small-RNA
sequencing contain the 3' sequencing adapter because the read is
longer than the molecule that is sequenced. Amplicon reads start with
a primer sequence. Poly-A tails are useful for pulling out RNA from
your sample, but often you don't want them to be in your reads.

Cutadapt helps with these trimming tasks by finding the adapter or
primer sequences in an error-tolerant way. It can also modify and
filter reads in various ways. Adapter sequences can contain IUPAC
wildcard characters. Also, paired-end reads and even colorspace data
is supported. If you want, you can also just demultiplex your input
data, without removing adapter sequences at all.

Cutadapt comes with an extensive suite of automated tests and is
available under the terms of the MIT license.

If you use cutadapt, please cite:
Marcel Martin. Cutadapt removes adapter sequences from high-throughput
sequencing reads. EMBnet.journal, 17(1):10-12, May 2011. DOI:
http://dx.doi.org/10.14806/ej.17.1.200