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!

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