Clean biological sequences from high-throughput sequencing reads

 Cutadapt helps with biological sequence clean 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.