trout 0.9.3

trout is a bioinformatics software package that uses suffix trees to compute the distances between genomes.

trout is a bioinformatics software package that uses suffix trees to compute the distances between genomes.

Setup

Build from source

wget https://bitbucket.org/NDBL/trout/get/trout-0.9.tar.gz
tar -xvzf trout-0.9.tar.gz
mv NDBL-trout-<commit> trout-0.9
cd trout-0.9
make

Requirements

• /usr/bin/make

• /usr/bin/g++

• /usr/bin/python

Usage

trout-suffix builds a suffix tree from a fastq and searches that tree for kmers to generate a binary sketch (.trout.sketch)

usage:    trout-suffix <input_fastq> <kmer_markers> <output_sketch>

trout-matrix generates a distance matrix from the binary sketches (.trout.sketch) produced by trout-suffix

usage:    trout-matrix <sketch_dir>

trout-compare computes the difference between two distance matrices

usage:    trout-compare <distance_matrix> <distance_matrix>

trout-match computes the number of matches of the kmer-markers across binary sketches (.trout.sketch)

usage:    trout-match <sketch_dir>

Example Usage

For an example usage with sample data:

make sample

To remove generated files when finished:

make sample-clean

Contact

Notre Dame Bioinformatics Lab

Will Markley: [e-mail]