tools for comparing DNA sequences with MinHash sketches
Quickly search, compare, and analyze genomic and metagenomic data sets.
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 (
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.
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
$ 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.
Please ask questions and files issues on Github.
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.
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.
sourmash/ directory contains the Python library and command-line interface code.
src/core/ directory contains the Rust library implementing core
Tests require py.test and can be run with
Please see the developer notes for more information on getting set up with a development environment.
CTB July 2020
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