tools for comparing biological sequences with k-mer sketches

Project description

sourmash

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

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
$ 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

Project details

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4.8.11

Jul 31, 2024

4.8.10

Jun 29, 2024

4.8.9

Jun 11, 2024

4.8.8

Apr 9, 2024

4.8.7

Mar 21, 2024

4.8.6

Feb 11, 2024

4.8.5

Dec 12, 2023

4.8.4

Sep 15, 2023

4.8.3

Aug 17, 2023

This version

4.8.2

Apr 20, 2023

4.8.1

Apr 17, 2023

4.8.0

Apr 6, 2023

4.7.0

Mar 3, 2023

4.6.1

Dec 3, 2022

4.6.0

Dec 2, 2022

4.5.0

Sep 7, 2022

4.5.0rc1 pre-release

Sep 7, 2022

4.4.3

Jul 24, 2022

4.4.2

Jul 19, 2022

4.4.1

Jul 9, 2022

4.4.0

May 13, 2022

4.3.0

Mar 11, 2022

4.2.4

Feb 5, 2022

4.2.3

Dec 20, 2021

4.2.2

Aug 11, 2021

4.2.1

Jul 17, 2021

4.2.0

Jul 1, 2021

4.1.2

Jun 7, 2021

4.1.1

May 22, 2021

4.1.0

May 14, 2021

4.0.0

Mar 2, 2021

4.0.0rc2 pre-release

Mar 2, 2021

4.0.0rc1 pre-release

Feb 18, 2021

4.0.0a3 pre-release

Dec 8, 2020

4.0.0a2 pre-release

Dec 8, 2020

4.0.0a1 pre-release

Nov 25, 2020

3.5.1

Feb 16, 2021

3.5.0

Aug 11, 2020

3.4.1

Jul 23, 2020

3.4.0

Jul 14, 2020

3.3.1

May 27, 2020

3.3.0

May 4, 2020

3.2.3

Apr 21, 2020

3.2.2

Feb 9, 2020

3.2.1

Feb 4, 2020

3.2.0

Jan 27, 2020

3.1.0

Jan 15, 2020

3.0.1

Jan 4, 2020

3.0.0

Jan 3, 2020

3.0.0rc1 pre-release

Dec 27, 2019

2.3.1

Dec 16, 2019

2.3.0

Nov 22, 2019

2.2.0

Sep 30, 2019

2.1.0

Aug 27, 2019

2.0.1

Jun 6, 2019

2.0.0

Mar 21, 2019

2.0.0a11 pre-release

Jan 4, 2019

2.0.0a10 pre-release

Oct 3, 2018

2.0.0a9 pre-release

Jul 23, 2018

2.0.0a8 pre-release

Jun 22, 2018

2.0.0a7 pre-release

Jun 22, 2018

2.0.0a6 pre-release

Jun 22, 2018

2.0.0a5 pre-release

Jun 22, 2018

2.0.0a4 pre-release

Jun 22, 2018

2.0.0a2 pre-release

Jun 22, 2018

1.0

Sep 13, 2016

0.9.6

Sep 11, 2016

0.9.5

Sep 11, 2016

0.9.4

Jul 12, 2016

0.9.4-rc1 pre-release

Jul 12, 2016

0.9.3

Jul 10, 2016

0.9.2

Jun 16, 2016

0.3

Jun 7, 2016

0.2

Apr 10, 2016

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