Hi, The Roche off instrument applications cover this (working directly with the SFF files). Try asking Edward Kkirton if he would update his "Suite of Newbler tools" wrappers in the Community Tool Shed to handle barcode trimming (and dividing SFF files by barcode). See http://community.g2.bx.psu.edu/ Alternatively, and maybe not quite what you need, I'm working on barcode/primer/adapter trimming for FASTA, FASTQ and SFF files - see this thread earlier this month on the Galaxy dev mailing list: http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-February/004344.html Peter