Hi all, Here's a patch that allow the Bowtie wrapper in Galaxy to use FASTA files and Illumina FASTQ files, without grooming. The input type is automatically detected (based on the dataset's type). The patch is also available here: http://cancan.cshl.edu/labmembers/gordon/files/galaxy_bowtie_wrapper_fasta_i... To import it, run: hg import http://cancan.cshl.edu/labmembers/gordon/files/galaxy_bowtie_wrapper_fasta_i... Comments are welcomed, -gordon