sourmash
There are 87 repositories under sourmash topic.
sourmash-bio/sourmash
Quickly search, compare, and analyze genomic and metagenomic data sets.
dib-lab/charcoal
Remove contaminated contigs from genomes using k-mers and taxonomies.
dib-lab/genome-grist
map Illumina metagenomes to genomes!
Arcadia-Science/sourmashconsumr
Working with the outputs of sourmash in R
luizirber/2018-python-rust
This work presents a way to write extensions in Rust and use them in Python, using sourmash as an example.
sourmash-bio/wort
A database for signatures of public genomic sources
sourmash-bio/sourmash_plugin_branchwater
fast, multithreaded sourmash operations: search, compare, and gather.
sourmash-bio/databases
Build sourmash databases for genbank.
dib-lab/2020-paper-sourmash-gather
Here we describe an extension of MinHash that permits accurate compositional analysis of metagenomes with low memory and disk requirements.
camillescott/goetia
Streaming de Bruijn and Compact de Bruijn Graph Algorithms
luizirber/2017-recomb
Poster presented at RECOMB 2017
sourmash-bio/branchwater
Searching large collections of sequencing data with genome-scale queries
dib-lab/distillerycats
Find disease associations across metagenomes with k-mers using sourmash, and then recover pangenomic accessory elements using spacegraphcats.
dib-lab/2021-paper-ibd
Meta-analysis of metagenomes via machine learning and assembly graphs reveals strain switches in Crohn’s disease
dib-lab/q2-sourmash
Qiime2 Sourmash Plugin
luizirber/2018-sms
Poster and talk presented at Bioinformatics for the Microbiome Symposium at Stanford on 2018-09-24
sourmash-bio/sourmash-mixers
A meta-package to install a number of sourmash plugins!
ctb/2024-human-contam
Explore microbial contamination in human whole-genome shotgun data sets, using sourmash
ctb/magsearch
Workflow and config files for searching (very) large public databases with sourmash sketches
ctb/sourmash_plugin_commonhash
sourmash plugin to filter hashes/k-mers by presence across many sketches
dib-lab/sourmash-oddify
Tools and workflows for evaluating bacterial and archaeal genome contamination with sourmash and GTDB.
luizirber/2020-cami
Preparing sourmash for CAMI 2 evaluations
ctb/2022-sourmash-uniqify
Greedy iterative clustering of genomes using sourmash
dib-lab/2019-sourmash-gtdb
Tools and scripts for studying the GTDB taxonomy with sourmash
dib-lab/2022-branchwater-benchmarking
Benchmarking etc code for https://dib-lab.github.io/2022-paper-branchwater-software/
EBI-Metagenomics/mgnify-sourmash-component
A web component that let you select FastA or FastQ sequence files and creates sketches (KmerMinHash signatures) using Sourmash.
luizirber/decoct
The essence of sourmash. An experimental CLI with a subset of the sourmash features, mainly used to drive development of features in the core library.
sourmash-bio/database-examples
Example workflows and useful scripts for building your own sourmash databases
sourmash-bio/sourmash-examples
Example commands for doing sequence analysis with sourmash
sourmash-bio/sourmash_plugin_sketchall
Sketch many files at once
sourmash-bio/sourmash_plugin_template
template for building sourmash plugins