khmer

bioinformatics bloom-filter count-min-sketch dna graph-traversal k-mer python

Score: 19.109213042305168

Last synced: about 21 hours ago
JSON representation

Repository metadata:

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

Host: GitHub
URL: https://github.com/dib-lab/khmer
Owner: dib-lab
License: other
Created: 2012-05-15T03:52:53.000Z (over 14 years ago)
Default Branch: master
Last Pushed: 2024-02-17T11:37:33.000Z (over 2 years ago)
Last Synced: 2026-09-19T08:17:21.366Z (9 days ago)
Topics: bioinformatics, bloom-filter, count-min-sketch, dna, graph-traversal, k-mer, python
Language: Python
Homepage: http://khmer.readthedocs.io/
Size: 50.4 MB
Stars: 789
Watchers: 67
Forks: 297
Open Issues: 353
Metadata Files:
- Readme: README.rst
- Changelog: CHANGELOG.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.rst
- Citation: CITATION
- Authors: authors.csv

Owner metadata:

Name: The Lab for Data Intensive Biology
Login: dib-lab
Email:
Kind: organization
Description: Previously "Genomics, Evolution, and Development Lab" @ Michigan State University
Website: http://ivory.idyll.org/lab/
Location: University of California, Davis, School of Veterinary Medicine, Davis, California, USA
Twitter:
Company:
Icon url: https://avatars.githubusercontent.com/u/1740697?v=4
Repositories: 176
Last Synced at: 2026-09-24T18:56:36.291Z
Profile URL: https://github.com/dib-lab

GitHub Events

Total

Fork event: 5
Watch event: 26
Total: 31

Last Year

Watch event: 4
Total: 4

Committers metadata

Last synced: 2 days ago

Total Commits: 5,159
Total Committers: 95
Avg Commits per committer: 54.305
Development Distribution Score (DDS): 0.635

Commits in past year: 0
Committers in past year: 0
Avg Commits per committer in past year: 0.0
Development Distribution Score (DDS) in past year: 0.0

Name	Email	Commits
C. Titus Brown	t**s@i**g	1882
Michael R. Crusoe	m**e@m**u	736
Camille Scott	c**w@g**m	432
Tim Head	b**m@g**m	299
Jake Fenton	b**f@g**m	249
Daniel Standage	d**e@g**m	246
Eric McDonald	e**m@m**u	229
Luiz Irber	l**r@g**m	186
Kevin Murray	s**m@k**u	185
Jason Pell	j**l@g**m	70
Tamer Mansour	d**r@g**m	50
Jordan Fish	j**h@g**m	41
Echelon9	r**d@g**m	35
Jessica Mizzi	m**s@m**u	29
Qingpeng	q**g@g**m	25
Scott Fay	s**y@i**m	25
Qingpeng Zhang	q**g@m**u	25
SusInMotion	s**g@g**m	22
Michael Wright	w**7@g**m	21
Justin Lippi	j**i@g**m	21
Ram RS	r**s@n**u	17
Adina	h**d@m**u	17
Thomas Fenzl	t**l@g**t	16
Sarah Guermond	s**d@g**m	16
bue	e**h@z**m	16
Sherine Awad	s**d@g**m	13
Andreas Härpfer	a**r@g**m	12
Shannon EK Joslin	s**n@u**u	12
leonorgg	l**z@w**k	11
Will Trimble	t**e@a**v	9
and 65 more...

Issue and Pull Request metadata

Last synced: 2 days ago

Total issues: 70
Total pull requests: 119
Average time to close issues: 6 months
Average time to close pull requests: 4 months
Total issue authors: 36
Total pull request authors: 24
Average comments per issue: 2.56
Average comments per pull request: 7.04
Merged pull request: 92
Bot issues: 0
Bot pull requests: 0

Past year issues: 0
Past year pull requests: 0
Past year average time to close issues: N/A
Past year average time to close pull requests: N/A
Past year issue authors: 0
Past year pull request authors: 0
Past year average comments per issue: 0
Past year average comments per pull request: 0
Past year merged pull request: 0
Past year bot issues: 0
Past year bot pull requests: 0

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/dib-lab/khmer

Top Issue Authors

standage (9)
ctb (8)
olgabot (6)
mr-c (5)
Canadatechmanufacturing (3)
fungs (3)
dkoslicki (2)
solshiferaw (2)
zmunro (2)
taranglute (2)
khuch123 (2)
bzvew (2)
ZhuangZK (1)
bwlang (1)
JuantonioMS (1)

Top Pull Request Authors

standage (23)
mr-c (22)
luizirber (12)
ctb (11)
SensibleSalmon (11)
camillescott (8)
shokrof (7)
betatim (5)
kdm9 (3)
wltrimbl (3)
jchow32 (1)
sanchestm (1)
Gnojoomi (1)
SherineAwad (1)
drtamermansour (1)

Top Issue Labels

low-hanging-fruit (7)
Documentation (4)
enhancement (2)
Python (2)
upstream bug (1)
Cython (1)
C++ (1)
theme:best-practices (1)
discussion-needed (1)
bug (1)
theme:customer-oriented (1)

Top Pull Request Labels

Ready For Review and Merge! (16)
Cython (3)
Documentation (2)
C++ (1)
Python (1)
discussion-needed (1)
bug (1)
Work In Progress (1)
low-hanging-fruit (1)
HyperLogLog counter (1)

Package metadata

Total packages: 2
Total downloads:
- pypi: 1,763 last-month
Total docker downloads: 45
Total dependent packages: 2 (may contain duplicates)
Total dependent repositories: 20 (may contain duplicates)
Total versions: 31
Total maintainers: 4

pypi.org: khmer

khmer k-mer counting library

Homepage: https://khmer.readthedocs.io/
Documentation: https://khmer.readthedocs.io/
Licenses: BSD License
Latest release: 2.1.1 (published over 8 years ago)
Last Synced: 2026-09-26T18:34:33.203Z (2 days ago)
Versions: 17
Dependent Packages: 2
Dependent Repositories: 20
Downloads: 1,763 Last month
Docker Downloads: 45
Rankings:
- Docker downloads count: 1.292%
- Dependent repos count: 3.253%
- Dependent packages count: 4.71%
- Average: 6.141%
- Downloads: 15.31%
Maintainers (4)

proxy.golang.org: github.com/dib-lab/khmer

Homepage:
Documentation: https://pkg.go.dev/github.com/dib-lab/khmer#section-documentation
Licenses: other
Latest release: v2.1.2+incompatible (published about 9 years ago)
Last Synced: 2026-09-26T18:34:35.797Z (2 days ago)
Versions: 14
Dependent Packages: 0
Dependent Repositories: 0
Rankings:
- Dependent packages count: 6.472%
- Average: 6.69%
- Dependent repos count: 6.908%

Dependencies

docker/Dockerfile docker

debian stable build

doc/requirements.txt pypi

guzzle_sphinx_theme ==0.7.11
setuptools >=3.4.1
sphinxcontrib-autoprogram >=0.1.4

setup.py pypi

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