Quickly search, compare, and analyze genomic and metagenomic data sets.
Remove contaminated contigs from genomes using k-mers and taxonomies.
This work presents a way to write extensions in Rust and use them in Python, using sourmash as an example.
A database for signatures of public genomic sources
fast, multithreaded sourmash operations: search, compare, and gather.
Searching large collections of sequencing data with genome-scale queries
Here we describe an extension of MinHash that permits accurate compositional analysis of metagenomes with low memory and disk requirements.
Poster presented at RECOMB 2017
Streaming de Bruijn and Compact de Bruijn Graph Algorithms
Find disease associations across metagenomes with k-mers using sourmash, and then recover pangenomic accessory elements using spacegraphcats.
Meta-analysis of metagenomes via machine learning and assembly graphs reveals strain switches in Crohn’s disease
Poster and talk presented at Bioinformatics for the Microbiome Symposium at Stanford on 2018-09-24
Workflow and config files for searching (very) large public databases with sourmash sketches
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