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        "author": "Will Markley",
        "author_email": "wmarkley@nd.edu",
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        "description": "Trout\n=====\n\n``trout`` is a bioinformatics software package that uses suffix trees to\ncompute the distances between genomes.\n\nSetup\n-----\n\nBuild from source\n~~~~~~~~~~~~~~~~~\n\n::\n\n    wget https://bitbucket.org/NDBL/trout/get/trout-0.9.tar.gz\n    tar -xvzf trout-0.9.tar.gz\n    mv NDBL-trout-<commit> trout-0.9\n    cd trout-0.9\n    make\n\nRequirements\n------------\n\n-  ``/usr/bin/make``\n-  ``/usr/bin/g++``\n-  ``/usr/bin/python``\n\nUsage\n-----\n\n``trout-suffix`` builds a suffix tree from a *fastq* and searches that\ntree for kmers to generate a binary sketch (*.trout.sketch*)\n\n::\n\n    usage:    trout-suffix <input_fastq> <kmer_markers> <output_sketch>\n\n``trout-matrix`` generates a distance matrix from the binary sketches\n(*.trout.sketch*) produced by ``trout-suffix``\n\n::\n\n    usage:    trout-matrix <sketch_dir>\n\n``trout-compare`` computes the difference between two distance matrices\n\n::\n\n    usage:    trout-compare <distance_matrix> <distance_matrix>\n\n``trout-match`` computes the number of matches of the kmer-markers\nacross binary sketches (*.trout.sketch*)\n\n::\n\n    usage:    trout-match <sketch_dir>\n\nExample Usage\n-------------\n\nFor an example usage with sample data:\n\n::\n\n    make sample\n\nTo remove generated files when finished:\n\n::\n\n    make sample-clean\n\nContact\n-------\n\n| `Notre Dame Bioinformatics\n  Lab <http://www.cse.nd.edu/~biocmp/index.html>`__\n| Will Markley: `wmarkley@nd.edu <mailto:%20wmarkley@nd.edu>`__",
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        "maintainer": "",
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        "name": "trout",
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