sourmash v4

sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets - Published in JOSS (2024)

https://github.com/sourmash-bio/sourmash

Science Score: 100.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 7 DOI reference(s) in README and JOSS metadata
✓
Academic publication links
Links to: joss.theoj.org
✓
Committers with academic emails
7 of 47 committers (14.9%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
Published in Journal of Open Source Software

Keywords

bioinformatics fracminhash hacktoberfest kmer minhash python rust scaled-minhash sketching sourmash taxonomic-classification taxonomic-profiling

Keywords from Contributors

dna bloom-filter count-min-sketch graph-traversal k-mer genomics parsing cryptocurrencies energy-systems physics

Last synced: 4 months ago · JSON representation ·

Repository

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

Basic Info

Host: GitHub
Owner: sourmash-bio
License: other
Language: Python
Default Branch: latest
Homepage: http://sourmash.readthedocs.io/en/latest/
Size: 47.2 MB

Statistics

Stars: 520
Watchers: 16
Forks: 87
Open Issues: 810
Releases: 72

Topics

bioinformatics fracminhash hacktoberfest kmer minhash python rust scaled-minhash sketching sourmash taxonomic-classification taxonomic-profiling

Created over 9 years ago · Last pushed 4 months ago

Metadata Files

Readme Contributing License Code of conduct Citation Codemeta Zenodo

sourmash

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

Usage:

sourmash sketch dna *.fq.gz
sourmash compare *.sig -o distances.cmp -k 31
sourmash plot distances.cmp

sourmash 1.0 is published on JOSS; please cite that paper if you use sourmash (doi: 10.21105/joss.06830):.

The latest major release is sourmash v4, which has several command-line and Python incompatibilities with previous versions. Please visit our migration guide to upgrade!

sourmash is a k-mer analysis multitool, and we aim to provide stable, robust programmatic and command-line APIs for a variety of sequence comparisons. Some of our special sauce includes: - FracMinHash sketching, which enables accurate comparisons (including ANI) between data sets of different sizes - sourmash gather, a combinatorial k-mer approach for more accurate metagenomic profiling

Please see the sourmash publications for details.

The name is a riff off of Mash, combined with @ctb's love of whiskey. (Sour mash is used in making whiskey.)

Maintainers: C. Titus Brown (@ctb), Luiz C. Irber, Jr (@luizirber), and N. Tessa Pierce-Ward (@bluegenes).

sourmash was initially developed by the Lab for Data-Intensive Biology at the UC Davis School of Veterinary Medicine, and now includes contributions from the global research and developer community.

Installation

We recommend using conda-forge to install sourmash:

conda install -c conda-forge sourmash-minimal This will install the latest stable version of sourmash 4.

You can also use pip to install sourmash:

pip install sourmash

A quickstart tutorial is available.

Requirements

sourmash runs under Python 3.11 and later on Windows, Mac OS X, and Linux. The base requirements are screed, cffi, numpy, matplotlib, and scipy. Conda will install everything necessary, and is our recommended installation method (see below).

Installation with conda

conda-forge is a community maintained channel for the conda package manager. installing conda, you can install sourmash by running:

bash $ conda create -n sourmash_env -c conda-forge sourmash-minimal $ conda activate sourmash_env $ sourmash --help

which will install the latest released version.

Support

For questions, please open an issue on Github, or ask in our chat.

Development

Development happens on github at sourmash-bio/sourmash.

sourmash is developed in Python and Rust, and you will need a Rust environment to build it; see the developer notes for our suggested development setup.

After installation, sourmash is the main command-line entry point; run it with python -m sourmash, or do pip install -e /path/to/repo to do a developer install in a virtual environment.

The sourmash/ directory contains the Python library and command-line interface code.

The src/core/ directory contains the Rust library implementing core functionality.

Tests require py.test and can be run with make test.

Please see the developer notes for more information on getting set up with a development environment.

CTB Jan 2024

Owner

Name: sourmash, for large-scale biological sequence search!
Login: sourmash-bio
Kind: organization

Website: https://sourmash.bio
Repositories: 20
Profile: https://github.com/sourmash-bio

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

JOSS Publication

sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets

Published

June 28, 2024

DOI

10.21105/joss.06830

Volume 9, Issue 98, Page 6830

Authors

Luiz Irber

University of California Davis, Davis, CA, United States of America

N. Tessa Pierce-Ward

University of California Davis, Davis, CA, United States of America

Mohamed Abuelanin

University of California Davis, Davis, CA, United States of America

Harriet Alexander

Woods Hole Oceanic Institution, Woods Hole, MA, Unites States of America

Abhishek Anant

No affiliation

Keya Barve

University of California Davis, Davis, CA, United States of America

Colton Baumler

University of California Davis, Davis, CA, United States of America

Olga Botvinnik

Chan-Zuckerberg Biohub, San Francisco, CA, United States of America

Phillip Brooks

University of California Davis, Davis, CA, United States of America

Daniel Dsouza

No affiliation

Laurent Gautier

No affiliation

Mahmudur Rahman Hera

Pennsylvania State University, University Park, PA, United States of America

Hannah Eve Houts

University of California Davis, Davis, CA, United States of America

Lisa K. Johnson

University of California Davis, Davis, CA, United States of America

Fabian Klötzl

Max Planck Institute for Evolutionary Biology, Plön, Germany

David Koslicki

Pennsylvania State University, University Park, PA, United States of America

Marisa Lim

University of California Davis, Davis, CA, United States of America

Ricky Lim

No affiliation

Bradley Nelson

No affiliation

Ivan Ogasawara

No affiliation

Taylor Reiter

University of California Davis, Davis, CA, United States of America

Camille Scott

University of California Davis, Davis, CA, United States of America

Andreas Sjödin

Swedish Defence Research Agency (FOI), Stockholm, Sweden

Daniel Standage

National Bioforensic Analysis Center, Fort Detrick, MD, United States of America

S. Joshua Swamidass

Washington University in St Louis, St Louis, MO, United States of America

Connor Tiffany

No affiliation

Pranathi Vemuri

Chan-Zuckerberg Biohub, San Francisco, CA, United States of America

Erik Young

University of California Davis, Davis, CA, United States of America

C. Titus Brown

University of California Davis, Davis, CA, United States of America

Editor

Kevin M. Moerman

Citation (CITATION.cff)

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- family-names: Abuelanin
  given-names: Mohamed
  orcid: "https://orcid.org/0000-0002-3419-4785"
- family-names: Alexander
  given-names: Harriet
  orcid: "https://orcid.org/0000-0003-1308-8008"
- family-names: Anant
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- family-names: Barve
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- family-names: Dsouza
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- family-names: Gautier
  given-names: Laurent
  orcid: "https://orcid.org/0000-0003-0638-3391"
- family-names: Rahman Hera
  given-names: Mahmudur
  orcid: "https://orcid.org/0000-0002-5992-9012"
- family-names: Houts
  given-names: Hannah Eve
  orcid: "https://orcid.org/0000-0002-7954-4793"
- family-names: Johnson
  given-names: Lisa K.
  orcid: "https://orcid.org/0000-0002-3600-7218"
- family-names: Klötzl
  given-names: Fabian
  orcid: "https://orcid.org/0000-0002-6930-0592"
- family-names: Koslicki
  given-names: David
  orcid: "https://orcid.org/0000-0002-0640-954X"
- family-names: Lim
  given-names: Marisa
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  given-names: Ricky
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  given-names: Taylor
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  given-names: Camille
  orcid: "https://orcid.org/0000-0001-8822-8779"
- family-names: Sjödin
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  given-names: Connor
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- family-names: Vemuri
  given-names: Pranathi
  orcid: "https://orcid.org/0000-0002-5748-9594"
- family-names: Young
  given-names: Erik
  orcid: "https://orcid.org/0000-0002-9195-9801"
- family-names: Brown
  given-names: C. Titus
  orcid: "https://orcid.org/0000-0001-6001-2677"
contact:
- family-names: Brown
  given-names: C. Titus
  orcid: "https://orcid.org/0000-0001-6001-2677"
doi: 10.5281/zenodo.11557883
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
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    given-names: Luiz
    orcid: "https://orcid.org/0000-0003-4371-9659"
  - family-names: Pierce-Ward
    given-names: N. Tessa
    orcid: "https://orcid.org/0000-0002-2942-5331"
  - family-names: Abuelanin
    given-names: Mohamed
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  - family-names: Alexander
    given-names: Harriet
    orcid: "https://orcid.org/0000-0003-1308-8008"
  - family-names: Anant
    given-names: Abhishek
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  - family-names: Barve
    given-names: Keya
    orcid: "https://orcid.org/0000-0003-3241-2117"
  - family-names: Baumler
    given-names: Colton
    orcid: "https://orcid.org/0000-0002-5926-7792"
  - family-names: Botvinnik
    given-names: Olga
    orcid: "https://orcid.org/0000-0003-4412-7970"
  - family-names: Brooks
    given-names: Phillip
    orcid: "https://orcid.org/0000-0003-3987-244X"
  - family-names: Dsouza
    given-names: Daniel
    orcid: "https://orcid.org/0000-0001-7843-8596"
  - family-names: Gautier
    given-names: Laurent
    orcid: "https://orcid.org/0000-0003-0638-3391"
  - family-names: Hera
    given-names: Mahmudur Rahman
    orcid: "https://orcid.org/0000-0002-5992-9012"
  - family-names: Houts
    given-names: Hannah Eve
    orcid: "https://orcid.org/0000-0002-7954-4793"
  - family-names: Johnson
    given-names: Lisa K.
    orcid: "https://orcid.org/0000-0002-3600-7218"
  - family-names: Klötzl
    given-names: Fabian
    orcid: "https://orcid.org/0000-0002-6930-0592"
  - family-names: Koslicki
    given-names: David
    orcid: "https://orcid.org/0000-0002-0640-954X"
  - family-names: Lim
    given-names: Marisa
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  - family-names: Lim
    given-names: Ricky
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  - family-names: Nelson
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  - family-names: Ogasawara
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    orcid: "https://orcid.org/0000-0001-5049-4289"
  - family-names: Reiter
    given-names: Taylor
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  - family-names: Scott
    given-names: Camille
    orcid: "https://orcid.org/0000-0001-8822-8779"
  - family-names: Sjödin
    given-names: Andreas
    orcid: "https://orcid.org/0000-0001-5350-4219"
  - family-names: Standage
    given-names: Daniel
    orcid: "https://orcid.org/0000-0003-0342-8531"
  - family-names: Swamidass
    given-names: S. Joshua
    orcid: "https://orcid.org/0000-0003-2191-0778"
  - family-names: Tiffany
    given-names: Connor
    orcid: "https://orcid.org/0000-0001-8188-7720"
  - family-names: Vemuri
    given-names: Pranathi
    orcid: "https://orcid.org/0000-0002-5748-9594"
  - family-names: Young
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  date-published: 2024-06-28
  doi: 10.21105/joss.06830
  issn: 2475-9066
  issue: 98
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6830
  title: "sourmash v4: A multitool to quickly search, compare, and
    analyze genomic and metagenomic data sets"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06830"
  volume: 9
title: "sourmash v4: A multitool to quickly search, compare, and analyze
  genomic and metagenomic data sets"

CodeMeta (codemeta.json)

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  "description": "Generate, compare, and manipulate MinHash sketches of genomic data",
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  "license": "BSD 3-clause",
  "title": "sourmash",
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}

Papers & Mentions

Total mentions: 10

PhyloMagnet: fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics

DOI: 10.1093/bioinformatics/btz799
OpenAlex ID: https://openalex.org/W2981778858
Published: October 2019

Last synced: 2 months ago

Complete Genome Sequence of Streptococcus agalactiae Strain 01173, Isolated from Kuwaiti Wild Fish

DOI: 10.1128/MRA.00674-20
OpenAlex ID: https://openalex.org/W3082367067
Published: September 2020

Last synced: 2 months ago

Streaming histogram sketching for rapid microbiome analytics

DOI: 10.1186/s40168-019-0653-2
OpenAlex ID: https://openalex.org/W2950044153
Published: March 2019

Last synced: 2 months ago

LINflow: a computational pipeline that combines an alignment-free with an alignment-based method to accelerate generation of similarity matrices for prokaryotic genomes

DOI: 10.7717/peerj.10906
OpenAlex ID: https://openalex.org/W3137842111
Published: March 2021

Last synced: 2 months ago

Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN)

DOI: 10.1371/journal.pcbi.1008716
OpenAlex ID: https://openalex.org/W3128393598
Published: February 2021

Last synced: 2 months ago

Large-scale sequence comparisons with sourmash

DOI: 10.12688/f1000research.19675.1
OpenAlex ID: https://openalex.org/W2955167895
Published: July 2019

Last synced: 2 months ago

When the levee breaks: a practical guide to sketching algorithms for processing the flood of genomic data

DOI: 10.1186/s13059-019-1809-x
OpenAlex ID: https://openalex.org/W2972805712
Published: September 2019

Last synced: 2 months ago

Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity

DOI: 10.1186/s13059-020-02066-4
OpenAlex ID: https://openalex.org/W3039380610
Published: July 2020

Last synced: 2 months ago

Metagenomic analysis of the cow, sheep, reindeer and red deer rumen

DOI: 10.1038/s41598-021-81668-9
OpenAlex ID: https://openalex.org/W3124816316
Published: January 2021

Last synced: 2 months ago

Freshwater <i>Chlorobia</i> Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations

DOI: 10.1128/mSystems.01196-20
OpenAlex ID: https://openalex.org/W3162831154
Published: June 2021

Last synced: 2 months ago

GitHub Events

Total

Create event: 235
Commit comment event: 1
Release event: 11
Issues event: 208
Watch event: 38
Delete event: 206
Issue comment event: 636
Push event: 768
Pull request event: 436
Pull request review comment event: 43
Pull request review event: 166
Fork event: 8

Last Year

Create event: 235
Commit comment event: 1
Release event: 11
Issues event: 208
Watch event: 38
Delete event: 206
Issue comment event: 636
Push event: 768
Pull request event: 437
Pull request review comment event: 43
Pull request review event: 166
Fork event: 8

Committers

Last synced: 5 months ago

All Time

Total Commits: 2,099
Total Committers: 47
Avg Commits per committer: 44.66
Development Distribution Score (DDS): 0.485

Past Year

Commits: 262
Committers: 9
Avg Commits per committer: 29.111
Development Distribution Score (DDS): 0.542

Top Committers

Name	Email	Commits
C. Titus Brown	t**s@i**g	1,080
dependabot[bot]	4****]	454
Luiz Irber	l****r	275
Tessa Pierce Ward	b****s	83
pre-commit-ci[bot]	6****]	51
Laurent Gautier	l**r@g**m	28
Keya Barve	5****e	22
Tim Head	b**m@g**m	12
Mohamed Abuelanin	m**n@g**m	10
Olga Botvinnik	o**k@g**m	8
Taylor Reiter	t**r@g**m	7
Erik Young	6****5	7
Pranathi Vemuri	p**i@g**m	5
dependabot-preview[bot]	2****]	4
brooksph	p**s@g**m	4
S. Joshua Swamidass	s**s@g**m	3
Michael R. Crusoe	1****c	3
ccbaumler	6****r	3
Hannah Eve Houts	4****s	3
Connor Tiffany	c**y@u**u	2
David Koslicki	d**i@g**m	2
Camille Scott	c**w@g**m	2
Connor Tiffany	c****u	2
Harriet Alexander	h**r@g**m	2
Luca Cappelletti	c**4@g**m	2
Peter Cock	p**k@g**m	2
Jason Stajich	j**d@g**m	2
Daniel Standage	d**e@n**v	2
pyup.io bot	g**t@p**o	1
ljcohen	l**n@u**u	1
and 17 more...

Committer Domains (Top 20 + Academic)

ucdavis.edu: 2 wustl.edu: 1 umich.edu: 1 evolbio.mpg.de: 1 yale.edu: 1 pyup.io: 1 nbacc.dhs.gov: 1 idyll.org: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 599
Total pull requests: 1,223
Average time to close issues: 11 months
Average time to close pull requests: 16 days
Total issue authors: 84
Total pull request authors: 20
Average comments per issue: 1.97
Average comments per pull request: 1.88
Merged pull requests: 972
Bot issues: 2
Bot pull requests: 699

Past Year

Issues: 167
Pull requests: 510
Average time to close issues: 18 days
Average time to close pull requests: 3 days
Issue authors: 29
Pull request authors: 8
Average comments per issue: 0.45
Average comments per pull request: 1.61
Merged pull requests: 382
Bot issues: 0
Bot pull requests: 309

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Top Authors

Issue Authors

ctb (388)
bluegenes (42)
mr-eyes (16)
luizirber (14)
ccbaumler (12)
taylorreiter (8)
jessicalumian (7)
yuzie0314 (5)
Amanda-Biocortex (5)
AnneliektH (5)
jorondo1 (4)
phiweger (3)
agombolay (3)
jodyphelan (3)
chunyuma (3)

Pull Request Authors

dependabot[bot] (609)
ctb (308)
luizirber (107)
pre-commit-ci[bot] (90)
bluegenes (75)
mr-c (6)
LucaCappelletti94 (6)
olgabot (5)
Glfrey (2)
magikcarp (2)
cmatKhan (2)
fossabot (2)
mr-eyes (2)
peterjc (1)
rialc13 (1)

Top Labels

Issue Labels

5.0 (41) doc (39) plugin_todo (22) rust (21) code (11) faq (11) fyi (10) enhancement (9) taxonomy (7) plugin (6) sbt (5) question (4) tutorial (4) md5sum (4) speeding-up-gather (4) good first issue (4) revisit_me (3) example (3) databases (2) use-case (2) idea (2) dependencies (2) python (2) developer_infrastructure (1) paper (1) videos (1) slides (1) talks (1) R (1) help wanted (1)

Pull Request Labels

dependencies (608) rust (452) github_actions (135) python (39) doc (1) plugin (1) msrv (1)

Packages

Total packages: 4
Total downloads:
- pypi 3,176 last-month
- cargo 43,103 total
- npm 57 last-month

Total dependent packages: 17
(may contain duplicates)
Total dependent repositories: 26
(may contain duplicates)
Total versions: 158
Total maintainers: 5

pypi.org: sourmash

tools for comparing biological sequences with k-mer sketches

Homepage: https://sourmash.bio/
Documentation: https://sourmash.readthedocs.io
License: other
Latest release: 4.9.4
published 5 months ago

Versions: 82
Dependent Packages: 15
Dependent Repositories: 21
Downloads: 3,176 Last month
Docker Downloads: 0

Rankings

Dependent packages count: 0.9%

Docker downloads count: 1.2%

Dependent repos count: 3.2%

Stargazers count: 3.2%

Average: 3.5%

Forks count: 5.0%

Downloads: 7.2%

Maintainers (3)

titus luizirber bluegenes

Last synced: 4 months ago

npmjs.org: sourmash

tools for comparing biological sequences with k-mer sketches

Homepage: https://github.com/sourmash-bio/sourmash#readme
License: BSD-3-Clause
Latest release: 0.19.0
published 11 months ago

Versions: 29
Dependent Packages: 1
Dependent Repositories: 2
Downloads: 57 Last month

Rankings

Stargazers count: 3.2%

Forks count: 3.4%

Downloads: 5.5%

Dependent repos count: 7.6%

Average: 8.1%

Dependent packages count: 21.0%

Maintainers (1)

luizirber

Last synced: 4 months ago

crates.io: sourmash

tools for comparing biological sequences with k-mer sketches

Documentation: https://docs.rs/sourmash/
License: BSD-3-Clause
Latest release: 0.21.0
published 6 months ago

Versions: 27
Dependent Packages: 1
Dependent Repositories: 2
Downloads: 43,103 Total

Rankings

Forks count: 7.5%

Stargazers count: 8.5%

Average: 13.1%

Dependent repos count: 13.2%

Downloads: 17.9%

Dependent packages count: 18.2%

Maintainers (2)

luizirber ctb

Last synced: 4 months ago

conda-forge.org: sourmash-minimal

This is a minimal version that avoids heavy dependencies and is as cross-platform as possible. For the complete version check the sourmash package in bioconda.

Homepage: https://github.com/sourmash-bio/sourmash
License: BSD-3-Clause
Latest release: 4.5.0
published over 3 years ago

Versions: 20
Dependent Packages: 0
Dependent Repositories: 1

Rankings

Stargazers count: 20.8%

Forks count: 22.5%

Dependent repos count: 24.4%

Average: 29.8%

Dependent packages count: 51.6%

Last synced: 4 months ago

Dependencies

.github/workflows/asv.yml actions

actions-rs/toolchain v1 composite
actions/checkout v3 composite
actions/setup-python v4 composite

.github/workflows/build_wheel.yml actions

actions/checkout v3 composite
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.github/workflows/build_wheel_all_archs.yml actions

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.github/workflows/dev_envs.yml actions

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.github/workflows/hypothesis.yml actions

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.github/workflows/metadata.yml actions

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.github/workflows/rust.yml actions

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Cargo.lock cargo

163 dependencies

src/core/Cargo.toml cargo

assert_matches 1.3.0 development
criterion 0.3.2 development
getrandom 0.2 development
needletail 0.4.1 development
proptest 1.0.0 development
rand 0.8.2 development
tempfile 3.1.0 development
az 1.0.0
bytecount 0.6.0
byteorder 1.4.3
cfg-if 1.0
counter 0.5.7
finch 0.5.0
fixedbitset 0.4.0
getset 0.1.1
log 0.4.8
md5 0.7.0
memmap2 0.5.8
murmurhash3 0.0.5
niffler 2.3.1
nohash-hasher 0.2.0
num-iter 0.1.43
once_cell 1.17.0
ouroboros 0.15.0
piz 0.4.0
primal-check 0.3.1
rayon 1.6.1
serde 1.0.152
serde_json 1.0.91
thiserror 1.0
twox-hash 1.6.0
typed-builder 0.11.0
vec-collections 0.3.4

binder/environment.yml pypi

matplotlib_venn *
mmh3 *

sourmash v4

Science Score: 100.0%

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README.md

sourmash

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JOSS Publication

sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets

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Papers & Mentions

PhyloMagnet: fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics

Complete Genome Sequence of Streptococcus agalactiae Strain 01173, Isolated from Kuwaiti Wild Fish

Streaming histogram sketching for rapid microbiome analytics

LINflow: a computational pipeline that combines an alignment-free with an alignment-based method to accelerate generation of similarity matrices for prokaryotic genomes

Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN)

Large-scale sequence comparisons with sourmash

When the levee breaks: a practical guide to sketching algorithms for processing the flood of genomic data

Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity

Metagenomic analysis of the cow, sheep, reindeer and red deer rumen

Freshwater <i>Chlorobia</i> Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations

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pypi.org: sourmash

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conda-forge.org: sourmash-minimal

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