Bioinformatics

Software

Genome Assembly Tools

  • readStepper.pl (Published name: extendFromReads.pl; citation: Hudson et al 2014) This script takes an Illumina read set and a short query, and performs a grep-trim-sort. Despite its simplicity it produces a powerful visualization of the matching reads, with multiple "horns" when the query is repeated in the genome. This is useful for resolving assembly problems.
  • extendMulti.pl
  • getMates.pl
  • denovo.pl
  • indexReads.pl

Islander Genomic Island Identification Suite

Juxtaposer: Software to detect single-strain mobile events in bacteria

tRNA and tmRNA Finder

  • tFind_1_4: tFind uses a combination of existing tools: tRNAscan-SE (Lowe and Eddy, 1997), BRUCE (Laslett et al. 2002) and ARAGORN (Laslett and Canback, 2004) to find and evaluate tmRNA, as well as our program rFind.pl, which includes our full- and terminus-sequence tmRNA databases which it searches using BLASTN. rFind.pl is directly used in this pipeline to find additional two-piece tmRNAs and accurately determine their termini and odd one-piece tmRNAs. These four programs are packaged together in tFind_1_4.tgz.
  • RapTOR, v2.0: pathogen detection in clinical samples through high-throughput sequencing