tools for comparing DNA sequences with MinHash sketches

These details have not been verified by PyPI

Project links

Homepage

Development Status
- 5 - Production/Stable
Environment
- Console
- MacOS X
Intended Audience
- Science/Research
License
- OSI Approved :: BSD License
Natural Language
- English
Operating System
- MacOS :: MacOS X
- POSIX :: Linux
Programming Language
Topic
- Scientific/Engineering :: Bio-Informatics

Project description

sourmash

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 -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.

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 -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.

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

Project details

These details have not been verified by PyPI

Project links

Homepage

Development Status
- 5 - Production/Stable
Environment
- Console
- MacOS X
Intended Audience
- Science/Research
License
- OSI Approved :: BSD License
Natural Language
- English
Operating System
- MacOS :: MacOS X
- POSIX :: Linux
Programming Language
Topic
- Scientific/Engineering :: Bio-Informatics

Release history Release notifications | RSS feed

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

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

This version

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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