Software Utilities

These software utilities were created at the University of Washington for research purposes. The scripts offered here are provided “as is” with no guarantee of performance or support, or completeness of documentation. Academic researchers are encouraged to freely use and modify them for research applications.

  • RunGATK.py - a utility for calling variants with the Broad Genome Analysis Toolkit
  • RunBowtie.py - a utility for running Bowtie, a Burrows-Wheeler aligner
  • FilterFastq2Fastq.pl - a utility for filtering sequencer reads based on quality
  • FilterFastq2Fasta.pl - a utility for filtering sequencer reads based on quality
  • ExtractBAMPositionCounts.py - a utility for counting the number of reads mapping to all reference positions in a BAM alignment file
  • Tn-seq - a pipeline for processing next-generation DNA sequence files (fastq files) generated by Tn-seq methods (transposon-insertion sequencing), a powerful technique for quantitatively profiling complex populations of transposon mutant bacteria (e.g., Gallagher et al. 2011. mBio.00315-10)