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sourmash

Quickly search, compare, and analyze genomic and metagenomic data sets.

Documentation Build Status Bioconda install PyPI codecov DOI License: 3-Clause BSD

Usage:

sourmash compute *.fq.gz
sourmash compare *.sig -o distances
sourmash plot distances

sourmash 1.0 is published on JOSS; please cite that paper if you use sourmash (doi: 10.21105/joss.00027):.

The name is a riff off of Mash, combined with @ctb's love of whiskey. (Sour mash is used in making whiskey.)

Primary authors: C. Titus Brown (@ctb) and Luiz C. Irber, Jr (@luizirber).

sourmash was initially developed by the Lab for Data-Intensive Biology at the UC Davis School of Veterinary Medicine, and now includes contributions from the global research and developer community.

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 3.

You can also use pip to install sourmash:

pip install sourmash

A quickstart tutorial is available.

Requirements

sourmash runs under both Python 2.7.x and Python 3.5+. The base requirements are screed, cffi, numpy, matplotlib, and scipy. Conda (see below) will install everything necessary, and is our recommended installation method.

Installation with conda

Bioconda is a channel for the conda package manager with a focus on bioinformatics software. After installing conda, you can install sourmash by running:

$ 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 released version.

Support

Please ask questions and files issues on Github.

Development

Development happens on github at dib-lab/sourmash.

sourmash is developed in Python and Rust, and you will need a Rust environment to build it; see the developer notes for our suggested development setup.

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 Python library and command-line interface code.

The src/core/ directory contains the Rust library implementing core functionality.

Tests require py.test and can be run with make test.

Please see the developer notes for more information on getting set up with a development environment.

CTB July 2020