Quickly search, compare, and analyze genomic and metagenomic data sets.
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Updated
Jun 11, 2024 - Python
Quickly search, compare, and analyze genomic and metagenomic data sets.
Poster presented at RECOMB 2017
Meta-analysis of metagenomes via machine learning and assembly graphs reveals strain switches in Crohn’s disease
A database for signatures of public genomic sources
Streaming de Bruijn and Compact de Bruijn Graph Algorithms
fast, multithreaded sourmash operations: search, compare, and gather.
Find disease associations across metagenomes with k-mers using sourmash, and then recover pangenomic accessory elements using spacegraphcats.
Poster and talk presented at Bioinformatics for the Microbiome Symposium at Stanford on 2018-09-24
Tools and workflows for evaluating bacterial and archaeal genome contamination with sourmash and GTDB.
Scripts that are useful for sourmash, but not necessarily part of the base command line.
Organizing notes and experiments around using sourmash in other languages (beside the supported one, Python).
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