github.com/dib-lab/sourmash ↗
Quickly search, compare, and analyze genomic and metagenomic data sets.
An animated visualization of dib-lab/sourmash's Git history from March 2016 to February 2021, built by 29 contributors. The codebase reached 6,086 lines, mostly Python. The video runs 2 minutes 33 seconds.
Render your own repo
Turn any GitHub repository into a video like this — free sample in seconds.
Open this visualization on its own page →
Language
Python
Contributors
29
Lines of Code
6,086
From
2016-03-25
To
2021-02-06
Advertisement
About dib-lab/sourmash
Sourmash is a bioinformatics tool for rapidly searching, comparing, and analyzing genomic and metagenomic datasets using k-mer sketching techniques. It implements specialized algorithms including FracMinHash sketching, which enables accurate comparisons between datasets of different sizes and can estimate Average Nucleotide Identity (ANI), as well as a gather command that uses combinatorial k-mer approaches for improved metagenomic profiling. The tool is named as a play on the Mash algorithm combined with a reference to sour mash whiskey.
The project is implemented primarily in Python with performance-critical components written in Rust, and is distributed through multiple package managers including conda-forge, pip, and Debian repositories. It provides both a command-line interface and programmatic Python API for sequence comparison workflows. Sourmash requires Python 3.11 or later and runs on Windows, macOS, and Linux, with core dependencies including numpy, scipy, matplotlib, screed, and cffi.
The project was initially developed at UC Davis's Lab for Data-Intensive Biology and is now maintained by a global community of contributors. Version 4 is the latest major release and includes significant API changes from previous versions. The tool has been formally published in the Journal of Open Source Software and is actively maintained with comprehensive documentation, tutorials, and community support channels available to users.
Advertisement