Genome Assembly Tools
(Published name: extendFromReads.pl; citation: Hudson et al 2014
[Supp Matls]) 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. We find this very useful for resolving assembly problems.
Islander Genomic Island Identification Suite
Juxtaposer: Software to detect single-strain mobile events in bacteria
- the software
- sample inputs and outputs
tFind_1_4 - (tRNA and tmRNA finder)
tFind uses a combination of existing tools: tRNAscan-SE
(Lowe and Eddy, 1997), BRUCE
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.
: pathogen detection in clinical samples through high-throughput sequencing