Metadata-Version: 1.1
Name: trout
Version: 0.9.1
Summary: trout is a bioinformatics software package that uses suffix trees to compute the distances between genomes. 
Home-page: https://bitbucket.org/NDBL/trout
Author: Will Markley
Author-email: wmarkley@nd.edu
License: UNKNOWN
Description: Trout
        =====
        
        ``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 <http://www.cse.nd.edu/~biocmp/index.html>`__
        | Will Markley: `wmarkley@nd.edu <mailto:%20wmarkley@nd.edu>`__
        
Keywords: genome distance metabarcoding
Platform: Linux
Platform: MacOS
Classifier: Intended Audience :: Science/Research
Classifier: Environment :: Console
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Operating System :: MacOS
Classifier: Operating System :: Unix
