khmer release v2.1: software for biological sequence analysis
khmer release v2.1: software for biological sequence analysis - Published in JOSS (2017)
https://github.com/dib-lab/khmer
Keywords
bioinformatics bloom-filter count-min-sketch dna graph-traversal k-mer python
Keywords from Contributors
taxonomic-classification genomics fracminhash kmer minhash scaled-minhash sketching sourmash taxonomic-profiling stable
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
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 13 years ago)
- Default Branch: master
- Last Pushed: 2024-02-17T11:37:33.000Z (almost 2 years ago)
- Last Synced: 2025-10-26T03:08:20.979Z (2 months 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: 782
- Watchers: 67
- Forks: 297
- Open Issues: 353
- Releases: 0
-
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: 104
- Last ynced at: 2023-03-24T01:56:50.587Z
- Profile URL: https://github.com/dib-lab
GitHub Events
Total
- Watch event: 22
- Fork event: 5
Last Year
- Watch event: 19
- Fork event: 5
Committers metadata
Last synced: 2 months ago
Total Commits: 5,159
Total Committers: 87
Avg Commits per committer: 59.299
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 | Commits | |
|---|---|---|
| C. Titus Brown | t****s@i****g | 1882 |
| Michael R. Crusoe | m****e@m****u | 738 |
| Camille Scott | c****w@g****m | 432 |
| Tim Head | b****m@g****m | 299 |
| Jacob Fenton | b****f@g****m | 249 |
| Daniel Standage | d****e@g****m | 246 |
| Eric McDonald | em@m****u | 232 |
| Kevin D. Murray | k****y@a****u | 186 |
| Luiz Irber | l****r@g****m | 186 |
| Jason Pell | j****l@g****m | 70 |
| Qingpeng Zhang | q****g@g****m | 50 |
| Tamer Mansour | d****r@g****m | 50 |
| Jordan Fish | j****h@g****m | 41 |
| Rhys Kidd | r****d@g****m | 35 |
| Jessica Mizzi | m****s@m****u | 29 |
| Scott Fay | s****y@g****m | 25 |
| Michael Wright | w****7@g****m | 24 |
| Susan R Steinman | s****n@g****m | 22 |
| Justin Lippi | j****i@g****m | 21 |
| Adina Howe | a****a@i****u | 17 |
| Ramakrishnan Srinivasan | r****s@n****u | 17 |
| Thomas Fenzl | t****l@g****t | 16 |
| Sarah Guermond | s****d@g****m | 16 |
| Elmar Bucher | b****e@o****u | 16 |
| Sherine Awad | d****d@u****u | 13 |
| Andreas Härpfer | a****r@g****m | 12 |
| Shannon EK Joslin | s****n@u****u | 12 |
| Leonor Garcia-Gutierrez | l****z@w****k | 11 |
| Benjamin Taylor | t****6@m****u | 9 |
| Will Trimble | t****e@a****v | 9 |
| and 57 more... | ||
Committer domains:
- msu.edu: 9
- ucdavis.edu: 5
- verdematics.com: 1
- tcd.ie: 1
- campus-048-222.ucdavis.edu: 1
- ip-10-123-79-75.ec2.internal: 1
- vort.org: 1
- oicr.on.ca: 1
- csp-macbookair3.roam.corp.google.com: 1
- mailaps.org: 1
- anl.gov: 1
- warwick.ac.uk: 1
- ohsu.edu: 1
- gmx.net: 1
- nyu.edu: 1
- iastate.edu: 1
- anu.edu.au: 1
- idyll.org: 1
- ip-10-113-37-240.ec2.internal: 1
- domu-12-31-39-18-07-ca.compute-1.internal: 1
- campus-053-033.ucdavis.edu: 1
- viper.lan: 1
- upr.edu: 1
- debian.org: 1
- dnaskittle.com: 1
- edvenson.com: 1
- umn.edu: 1
- addgene.org: 1
- rallydev.com: 1
- ip-10-87-85-207.ec2.internal: 1
- cornell.edu: 1
- cs.umd.edu: 1
- asu.edu: 1
- stlcop.edu: 1
- ibv.uio.no: 1
- manchester.ac.uk: 1
Issue and Pull Request metadata
Last synced: 4 months ago
Total issues: 70
Total pull requests: 48
Average time to close issues: 6 months
Average time to close pull requests: 11 months
Total issue authors: 36
Total pull request authors: 19
Average comments per issue: 2.66
Average comments per pull request: 2.98
Merged pull request: 22
Bot issues: 0
Bot pull requests: 0
Past year issues: 1
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: 1
Past year pull request authors: 0
Past year average comments per issue: 4.0
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
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 (18)
- shokrof (7)
- mr-c (5)
- luizirber (3)
- camillescott (2)
- jchow32 (1)
- sanchestm (1)
- Gnojoomi (1)
- drtamermansour (1)
- ctSkennerton (1)
- ogayot (1)
- wltrimbl (1)
- ryfi (1)
- ctb (1)
- jts (1)
Top Issue Labels
- low-hanging-fruit (7)
- Documentation (4)
- enhancement (2)
- Python (2)
- theme:customer-oriented (1)
- Cython (1)
- C++ (1)
- discussion-needed (1)
- upstream bug (1)
- theme:best-practices (1)
- bug (1)
Top Pull Request Labels
- Ready For Review and Merge! (12)
- Cython (2)
- Documentation (2)
- C++ (1)
- Work In Progress (1)
- bug (1)
- discussion-needed (1)
Package metadata
- Total packages: 2
-
Total downloads:
- pypi: 3,383 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 7 years ago)
- Last Synced: 2025-10-26T03:08:08.661Z (2 months ago)
- Versions: 17
- Dependent Packages: 2
- Dependent Repositories: 20
- Downloads: 3,383 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 over 8 years ago)
- Last Synced: 2025-10-26T03:08:02.979Z (2 months ago)
- Versions: 14
- Dependent Packages: 0
- Dependent Repositories: 0
-
Rankings:
- Dependent packages count: 6.472%
- Average: 6.69%
- Dependent repos count: 6.908%
Score: 19.647873784771857