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