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sourmash

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

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

Usage:

sourmash sketch dna *.fq.gz
sourmash compare *.sig -o distances.cmp -k 31
sourmash plot distances.cmp

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

The latest major release is sourmash v4, which has several command-line and Python incompatibilities with previous versions. Please visit our migration guide to upgrade!


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 4.

You can also use pip to install sourmash:

pip install sourmash

A quickstart tutorial is available.

Requirements

sourmash runs under Python 3.7 and later. 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 --help

which will install the latest released version.

Support

For questions, please open an issue on Github, or ask in our chat.

Development

Development happens on github at sourmash-bio/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.

Research notice

Please note that this repository is participating in a study into sustainability of open source projects. Data will be gathered about this repository for approximately the next 12 months, starting from 2021-06-11.

Data collected will include number of contributors, number of PRs, time taken to close/merge these PRs, and issues closed.

For more information, please visit our informational page or download our participant information sheet.


CTB Feb 2021