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!


On Thu, Feb 3, 2011 at 7:54 PM, Peter Cock <p.j.a.c...@googlemail.com>wrote:

> Hi all,
>
> I'm currently working with some 454 data where the sample was
> amplified with selective primers, and therefore the reads need a
> little processing to remove the primer sequences before assembly
> or mapping (something that sff_extract cleverly spots and warns
> the user about when doing an SFF to FASTA/FASTQ conversion).
>
> The actual processing I want to do is very similar to spotting
> and removing barcodes or adapters - except that PRC primers
> are often degenerate, i.e. have an N in them representing the
> fact it is a pool of primers covering A, C, G and T at that point,
> and primers may come in pairs.
>
> Looking over the provided tools in Galaxy, the only relevant ones
> I saw are as follows:
>
> emboss_5/emboss_primersearch.xml - the text output does not
> look helpful for trimming my sequences - nothing else in Galaxy
> uses this format, does it?
>
_______________________________________________
galaxy-dev mailing list
galaxy-dev@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev

Reply via email to