Quickly search, compare, and analyze genomic and metagenomic data sets.
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 (
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!
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.
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.
$ 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.
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.
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.
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.
CTB Feb 2021