Metadata-Version: 2.1
Name: sourmash
Version: 2.1.0
Summary: tools for comparing DNA sequences with MinHash sketches
Home-page: https://github.com/dib-lab/sourmash
Author: C. Titus Brown
Author-email: titus@idyll.org
License: BSD 3-clause
Description: # sourmash
        
        [![Documentation](https://readthedocs.org/projects/sourmash/badge/?version=latest)](http://sourmash.readthedocs.io/en/latest/)
        [![Build Status](https://travis-ci.com/dib-lab/sourmash.svg?branch=master)](https://travis-ci.com/dib-lab/sourmash)
        [![codecov](https://codecov.io/gh/dib-lab/sourmash/branch/master/graph/badge.svg)](https://codecov.io/gh/dib-lab/sourmash)
        [![DOI](http://joss.theoj.org/papers/10.21105/joss.00027/status.svg)](http://joss.theoj.org/papers/10.21105/joss.00027)
        
        Compute MinHash signatures for nucleotide (DNA/RNA) and protein sequences.
        
        Usage:
        
            sourmash compute *.fq.gz
            sourmash compare *.sig -o distances
            sourmash plot distances
        
        Sourmash 1.0 is [published on JOSS](https://doi.org/10.21105/joss.00027); please cite that paper if you use sourmash (`doi: 10.21105/joss.00027`):.
        
        ----
        
        The name is a riff off of [Mash](https://github.com/marbl/Mash),
        combined with @ctb's love of whiskey.
        ([Sour mash](https://en.wikipedia.org/wiki/Sour_mash) is used in
        making whiskey.)
        
        Primary authors: [C. Titus Brown](mailto:titus@idyll.org) ([@ctb](http://github.com/ctb)) and [Luiz C. Irber, Jr](mailto:sourmash@luizirber.org) ([@luizirber](http://github.com/luizirber)).
        
        sourmash is a product of the
        [Lab for Data-Intensive Biology](http://ivory.idyll.org/lab/) at the
        [UC Davis School of Veterinary Medicine](http://www.vetmed.ucdavis.edu).
        
        ## Installation
        
        We recommend using bioconda to install sourmash:
        
        ```
        conda install -c conda-forge -c bioconda sourmash
        ```
        This will install the latest stable version of sourmash 2.
        
        You can also use pip to install sourmash:
        
        ```
        pip install sourmash
        ```
        
        A quickstart tutorial [is available](https://sourmash.readthedocs.io/en/latest/tutorials.html).
        
        ### Requirements
        
        sourmash runs under both Python 2.7.x and Python 3.5+.  The base
        requirements are screed and ijson, together with a C++ development
        environment and the CPython development headers and libraries (for the
        C++ extension).
        
        The comparison code (`sourmash compare`) uses numpy, and the plotting
        code uses matplotlib and scipy, but most of the code is usable without
        these.
        
        For `search` and `gather` you also need `khmer` version 2.1+.
        
        ### Installation with conda
        
        Bioconda is a channel for the [conda](http://conda.pydata.org/docs/intro.html) package manager with a focus on bioinformatics software. After installing conda you will need to add the bioconda channel as well as the [other channels](https://bioconda.github.io/index.html#set-up-channels) bioconda depends on. Once you have setup bioconda, you can install sourmash by running:
        
        ```bash
        $ conda create -n sourmash_env -c conda-forge -c bioconda sourmash python=3.7
        $ source activate sourmash_env
        $ sourmash compute -h
        ```
        
        which will install the latest alpha release.
        
        ## Support
        
        Please ask questions and files issues
        [on Github](https://github.com/dib-lab/sourmash/issues).
        
        ## Development
        
        Development happens on github at
        [dib-lab/sourmash](https://github.com/dib-lab/sourmash).
        
        After installation, `sourmash` is the main command-line entry point;
        run it with `python -m sourmash`, or do `pip install -e /path/to/repo` to
        do a developer install in a virtual environment.
        
        The `sourmash/` directory contains the library code.
        
        Tests require py.test and can be run with `make test`.
        
        Please see [the developer notes](doc/developer.md) for more information.
        
        ----
        
        CTB
        Dec 2018
        
Platform: UNKNOWN
Classifier: Environment :: Console
Classifier: Environment :: MacOS X
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Programming Language :: C++
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Development Status :: 5 - Production/Stable
Description-Content-Type: text/markdown
Provides-Extra: test
Provides-Extra: demo
Provides-Extra: doc
Provides-Extra: 10x
