Hi Greg, Is there anything left of the old (pre-hg) Tool Shed? I'm wondering if I ever uploaded this tool back in early 2011, in which case could it have got lost in the migration to the current hg-based Tool Shed?: https://bitbucket.org/peterjc/galaxy-central/src/tools/tools/primers/seq_pri... https://bitbucket.org/peterjc/galaxy-central/src/tools/tools/primers/seq_pri... https://bitbucket.org/peterjc/galaxy-central/src/tools/tools/primers/seq_pri... <tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.7"> <description>Trim off 5' or 3' primers</description> <command interpreter="python"> seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file </command> ... If searching the archives is a hassle, don't worry - I'm just curious. Another likely explanation is simply that I never upload the tool - it was written for a Roche 454 dataset (to remove SMART primers) and could work directly on the SFF files. Unfortunately it is probably too slow to use on large Illumina FASTQ files. I might as well (re)post it to the Tool Shed now, perhaps with a warning that it is intended for smaller Roche/IonTorrent/Sanger sized datasets. Thanks, Peter