Flexbar
flexible barcode and adapter removal for sequencing platforms
...Flexbar supports next-generation sequencing data in fasta and fastq format, e.g. from the Illumina platform.
Reference:
Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar — flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012, 1(3):895-905.