What it does

Looks for the given primer sequences (within the existing clipped sequence) and further clips the reads to remove the primers and any preceding/trailing sequence.

Reads containing a forward primer are reduced to just the sequence after (and excluding) the forward primer.

Reads containing a reverse primer are reduced to just the sequence before (and excluding) the reverse primer.

Degenerate primers can be specified using the standard IUPAC ambiguity codes, thus a primer with an N would match A, C, T or G (or any of the IUPAC ambiguity codes) and so on.

Note that for SFF files only the clip/trim positions are edited - you will still be able to extract the original full read (with any adapter sequence and poor quality sequence) if you need to.

Note. This tool was initially written for Roche 454 data, and should also work fine on Sanger or Ion Torrent as well. However, it is probably too slow for use on large Illumina datasets.

Citation

This tool uses Biopython. If you use this tool in scientific work leading to a publication, please cite:

Cock et al 2009. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. https://doi.org/10.1093/bioinformatics/btp163 pmid:19304878.

This tool is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip