ucdavis-bioinformatics/scythe — pull request #2 by jfass (2012-08-22 23:15:07+00:00)
Title: new helper script to profile indexes in forward read-contaminating TruSeq adapter

added profileTruSeqIDs.pl, that can be run on a set of (TruSeq) forward reads, looks for exact matches to first ~30bp of adapter, then pulls out the 6bp index / ID / barcode, and counts and sorts them, to allow you to find the most frequent indices (which presumably are the sample indices).