sourmash

Quickly search, compare, and analyze genomic and metagenomic data sets.

Remove contaminated contigs from genomes using k-mers and taxonomies.

map Illumina metagenomes to genomes!

Working with the outputs of sourmash in R

fast, multithreaded sourmash operations: search, compare, and gather.

Searching large collections of sequencing data with genome-scale queries

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

Build sourmash databases for genbank.

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

Qiime2 Sourmash Plugin

Improved plotting/viz and cluster examination for sourmash

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

A meta-package to install a number of sourmash plugins!

Poster and talk presented at Bioinformatics for the Microbiome Symposium at Stanford on 2018-09-24