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 <[email protected]>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? >
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