tools for comparing DNA sequences with MinHash sketches

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Project description

sourmash

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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; 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 is a product of the Lab for Data-Intensive Biology at the UC Davis School of Veterinary Medicine.

Installation

We recommend using bioconda to install sourmash:

conda install sourmash

This will install the 2.0 pre-release series.

You can also use pip to install the pre-release like so:

pip install --pre sourmash

A quickstart tutorial is available.

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 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 bioconda depends on. Once you have setup bioconda, you can install sourmash by running:

$ conda create -n sourmash_env sourmash python=3.6.4
$ source activate sourmash_env
$ sourmash compute -h

which will install the latest alpha release.

Support

Please ask questions and files issues on Github.

Development

Development happens on github at 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 for more information.

CTB Dec 2018

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Release history Release notifications | RSS feed

4.8.11

4.8.10

4.8.9

4.8.8

4.8.7

4.8.6

4.8.5

4.8.4

4.8.3

4.8.2

4.8.1

4.8.0

4.7.0

4.6.1

4.6.0

4.5.0

4.5.0rc1 pre-release

4.4.3

4.4.2

4.4.1

4.4.0

4.3.0

4.2.4

4.2.3

4.2.2

4.2.1

4.2.0

4.1.2

4.1.1

4.1.0

4.0.0

4.0.0rc2 pre-release

4.0.0rc1 pre-release

4.0.0a3 pre-release

4.0.0a2 pre-release

4.0.0a1 pre-release

3.5.1

3.5.0

3.4.1

3.4.0

3.3.1

3.3.0

3.2.3

3.2.2

3.2.1

3.2.0

3.1.0

3.0.1

3.0.0

3.0.0rc1 pre-release

2.3.1

2.3.0

2.2.0

2.1.0

2.0.1

This version

2.0.0

2.0.0a11 pre-release

2.0.0a10 pre-release

2.0.0a9 pre-release

2.0.0a8 pre-release

2.0.0a7 pre-release

2.0.0a6 pre-release

2.0.0a5 pre-release

2.0.0a4 pre-release

2.0.0a2 pre-release

1.0

0.9.6

0.9.5

0.9.4

0.9.4-rc1 pre-release

0.9.3

0.9.2

0.3

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