Skip to main content

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

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

trout-0.9.3.tar.gz (32.0 kB view hashes)

Uploaded source

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page