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

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

Keywords

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

Keywords from Contributors

conda package-management genome notebook measurements transformer closember metagenomics parallel ecology

Last synced: 2 months ago
JSON representation

Acceptance Criteria

Revelant topics? true
External users? true
Open source license? true
Active? true
Fork? false

Repository metadata

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

Host: GitHub
URL: https://github.com/sourmash-bio/sourmash
Owner: sourmash-bio
License: other
Created: 2016-04-09T17:35:30.000Z (over 9 years ago)
Default Branch: latest
Last Pushed: 2025-10-20T23:40:58.000Z (2 months ago)
Last Synced: 2025-10-21T20:07:32.841Z (2 months ago)
Topics: bioinformatics, fracminhash, hacktoberfest, kmer, minhash, python, rust, scaled-minhash, sketching, sourmash, taxonomic-classification, taxonomic-profiling
Language: Python
Homepage: http://sourmash.readthedocs.io/en/latest/
Size: 47.2 MB
Stars: 524
Watchers: 16
Forks: 88
Open Issues: 815
Releases: 0
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.rst
- Citation: CITATION.cff
- Codemeta: codemeta.json
- Zenodo: .zenodo.json

Owner metadata

Name: sourmash, for large-scale biological sequence search!
Login: sourmash-bio
Email:
Kind: organization
Description: Quickly search, compare, and analyze genomic and metagenomic data sets.
Website: https://sourmash.bio
Location:
Twitter:
Company:
Icon url: https://avatars.githubusercontent.com/u/59402508?v=4
Repositories: 20
Last ynced at: 2023-03-03T23:19:54.194Z
Profile URL: https://github.com/sourmash-bio

GitHub Events

Total

Create event: 245
Commit comment event: 1
Release event: 11
Issues event: 218
Watch event: 40
Delete event: 212
Issue comment event: 673
Push event: 792
Pull request event: 459
Pull request review comment event: 44
Pull request review event: 171
Fork event: 8

Last Year

Create event: 238
Commit comment event: 1
Release event: 11
Issues event: 212
Watch event: 39
Delete event: 206
Issue comment event: 665
Push event: 779
Pull request review comment event: 43
Pull request review event: 166
Pull request event: 447
Fork event: 8

Committers metadata

Last synced: 2 months ago

Total Commits: 2,136
Total Committers: 47
Avg Commits per committer: 45.447
Development Distribution Score (DDS): 0.491

Commits in past year: 249
Committers in past year: 8
Avg Commits per committer in past year: 31.125
Development Distribution Score (DDS) in past year: 0.554

Name	Email	Commits
C. Titus Brown	t**s@i**g	1088
dependabot[bot]	4****]	469
Luiz Irber	l****r	278
Tessa Pierce Ward	b****s	83
pre-commit-ci[bot]	6****]	62
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
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brooksph	p**s@g**m	4
S. Joshua Swamidass	s**s@g**m	3
ccbaumler	6****r	3
Michael R. Crusoe	1****c	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
Daniel Standage	d**e@g**m	2
Jason Stajich	j**h@u**u	2
pyup.io bot	g**t@p**o	1
ljcohen	l**n@u**u	1
and 17 more...

Committer domains:

Issue and Pull Request metadata

Last synced: 2 months ago

Total issues: 607
Total pull requests: 1,251
Average time to close issues: 10 months
Average time to close pull requests: 16 days
Total issue authors: 84
Total pull request authors: 20
Average comments per issue: 1.98
Average comments per pull request: 1.88
Merged pull request: 990
Bot issues: 3
Bot pull requests: 716

Past year issues: 166
Past year pull requests: 476
Past year average time to close issues: 23 days
Past year average time to close pull requests: 3 days
Past year issue authors: 31
Past year pull request authors: 9
Past year average comments per issue: 0.54
Past year average comments per pull request: 1.59
Past year merged pull request: 353
Past year bot issues: 1
Past year bot pull requests: 283

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/sourmash-bio/sourmash

Top Issue Authors

ctb (392)
bluegenes (42)
mr-eyes (16)
luizirber (14)
ccbaumler (13)
taylorreiter (8)
jessicalumian (7)
AnneliektH (6)
yuzie0314 (5)
Amanda-Biocortex (5)
jorondo1 (4)
jodyphelan (4)
phiweger (3)
agombolay (3)
chunyuma (3)

Top Pull Request Authors

dependabot[bot] (622)
ctb (315)
luizirber (107)
pre-commit-ci[bot] (94)
bluegenes (77)
mr-c (6)
LucaCappelletti94 (6)
olgabot (5)
ccbaumler (3)
Glfrey (2)
magikcarp (2)
fossabot (2)
cmatKhan (2)
mr-eyes (2)
peterjc (1)

Top Issue Labels

5.0 (41)
doc (39)
rust (22)
plugin_todo (22)
code (13)
faq (11)
fyi (10)
enhancement (9)
taxonomy (7)
plugin (6)
sbt (5)
tutorial (4)
good first issue (4)
speeding-up-gather (4)
md5sum (4)
question (4)
dependencies (3)
revisit_me (3)
example (3)
databases (2)
use-case (2)
python (2)
idea (2)
developer_infrastructure (1)
paper (1)
videos (1)
slides (1)
talks (1)
R (1)
help wanted (1)

Top Pull Request Labels

dependencies (621)
rust (458)
github_actions (141)
python (40)
doc (1)
plugin (1)
msrv (1)

Package metadata

Total packages: 4
Total downloads:
- cargo: 46,605 total
- pypi: 9,667 last-month
- npm: 417 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
Licenses: other
Latest release: 4.9.4 (published 5 months ago)
Last Synced: 2025-10-26T03:17:49.783Z (2 months ago)
Versions: 82
Dependent Packages: 15
Dependent Repositories: 21
Downloads: 9,667 Last month
Docker Downloads: 0
Rankings:
- Dependent packages count: 0.902%
- Docker downloads count: 1.237%
- Dependent repos count: 3.163%
- Stargazers count: 3.246%
- Average: 3.46%
- Forks count: 5.049%
- Downloads: 7.162%
Maintainers (3)

npmjs.org: sourmash

tools for comparing biological sequences with k-mer sketches

Homepage: https://github.com/sourmash-bio/sourmash#readme
Licenses: BSD-3-Clause
Latest release: 0.19.0 (published 11 months ago)
Last Synced: 2025-10-26T03:17:50.678Z (2 months ago)
Versions: 29
Dependent Packages: 1
Dependent Repositories: 2
Downloads: 417 Last month
Rankings:
- Stargazers count: 3.224%
- Forks count: 3.361%
- Downloads: 5.506%
- Dependent repos count: 7.638%
- Average: 8.139%
- Dependent packages count: 20.968%
Maintainers (1)
- luizirber

crates.io: sourmash

tools for comparing biological sequences with k-mer sketches

Homepage:
Documentation: https://docs.rs/sourmash/
Licenses: BSD-3-Clause
Latest release: 0.21.0 (published 6 months ago)
Last Synced: 2025-10-26T03:18:16.971Z (2 months ago)
Versions: 27
Dependent Packages: 1
Dependent Repositories: 2
Downloads: 46,605 Total
Rankings:
- Forks count: 7.543%
- Stargazers count: 8.528%
- Average: 13.074%
- Dependent repos count: 13.204%
- Downloads: 17.91%
- Dependent packages count: 18.187%
Maintainers (2)
- luizirber
- ctb

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
Licenses: BSD-3-Clause
Latest release: 4.5.0 (published over 3 years ago)
Last Synced: 2025-10-26T03:18:49.481Z (2 months ago)
Versions: 20
Dependent Packages: 0
Dependent Repositories: 1
Rankings:
- Stargazers count: 20.829%
- Forks count: 22.541%
- Dependent repos count: 24.377%
- Average: 29.834%
- Dependent packages count: 51.589%

Dependencies

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Cargo.lock cargo

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src/core/Cargo.toml cargo

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binder/environment.yml pypi

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

Keywords

Keywords from Contributors

Acceptance Criteria

Repository metadata

Owner metadata

GitHub Events

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Last Year

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Issue and Pull Request metadata

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Package metadata

pypi.org: sourmash

npmjs.org: sourmash

crates.io: sourmash

conda-forge.org: sourmash-minimal

Dependencies