Have you looked at <br><a href="http://code.google.com/p/cutadapt/">http://code.google.com/p/cutadapt/</a><br>Features<br><ul><li>Gapped alignment with mismatches and indels, that is, errors in the adapter are tolerated </li>

<li>Finds adapters both in the 5&#39; and 3&#39; ends of reads </li><li>Accepts FASTQ, FASTA or .csfasta and .qual files (for AB SOLiD data) </li><li>Any input or output file can be gzip-compressed </li><li>Outputs FASTA or FASTQ </li>

<li>Trims color space reads correctly </li><li>Optionally removes primer base in color space data </li><li>Can produce MAQ- or BWA-compatible output </li></ul><br>only had the chance to play around with this for a while. but looks promising!<br>

<br><br><div class="gmail_quote">On Thu, Feb 3, 2011 at 7:54 PM, Peter Cock <span dir="ltr">&lt;<a href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">

Hi all,<br>
<br>
I&#39;m currently working with some 454 data where the sample was<br>
amplified with selective primers, and therefore the reads need a<br>
little processing to remove the primer sequences before assembly<br>
or mapping (something that sff_extract cleverly spots and warns<br>
the user about when doing an SFF to FASTA/FASTQ conversion).<br>
<br>
The actual processing I want to do is very similar to spotting<br>
and removing barcodes or adapters - except that PRC primers<br>
are often degenerate, i.e. have an N in them representing the<br>
fact it is a pool of primers covering A, C, G and T at that point,<br>
and primers may come in pairs.<br>
<br>
Looking over the provided tools in Galaxy, the only relevant ones<br>
I saw are as follows:<br>
<br>
emboss_5/emboss_primersearch.xml - the text output does not<br>
look helpful for trimming my sequences - nothing else in Galaxy<br>
uses this format, does it?<br>
</blockquote></div><br>