On Tue, Feb 8, 2011 at 8:15 AM, Kevin Lam <abou...@gmail.com> wrote: > Have you looked at > http://code.google.com/p/cutadapt/ > Features > > Gapped alignment with mismatches and indels, that is, errors in the adapter > are tolerated > Finds adapters both in the 5' and 3' ends of reads > Accepts FASTQ, FASTA or .csfasta and .qual files (for AB SOLiD data) > Any input or output file can be gzip-compressed > Outputs FASTA or FASTQ > Trims color space reads correctly > Optionally removes primer base in color space data > Can produce MAQ- or BWA-compatible output > > only had the chance to play around with this for a while. but looks > promising!
Hi Kevin, Thanks for the link - I think I skimmed over all the source code (its in Python + C which is nice from my personal perspective), and I'm pretty sure it does NOT handle ambiguous IUPAC codes (either in the adapter/barcode/primer or the read sequences). For the particular task I'm working on I do have degenerate PCR primers, i.e. they have N's in them representing the fact it is a pool of primers covering A, C, G and T at that point. This would be pretty strange for an adapter or barcode! Peter _______________________________________________ galaxy-dev mailing list firstname.lastname@example.org http://lists.bx.psu.edu/listinfo/galaxy-dev