Nextclade: clade assignment, mutation calling and quality control for viral genomes
Nextclade: clade assignment, mutation calling and quality control for viral genomes - Published in JOSS (2021)
https://github.com/nextstrain/nextclade
Keywords
clade clades coronavirus covid covid-19 covid19 dna influenza ncov neherlab next-generation-sequencing nextstrain research rna sars-cov-2 science sequences sequencing strain virus
Keywords from Contributors
bioinformatics package-management genomics conda annotation phylogenetics archived report measurements conversation
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
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
- Host: GitHub
- URL: https://github.com/nextstrain/nextclade
- Owner: nextstrain
- License: mit
- Created: 2020-06-12T13:01:14.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2025-10-17T14:03:12.000Z (2 months ago)
- Last Synced: 2025-10-26T01:34:27.651Z (2 months ago)
- Topics: clade, clades, coronavirus, covid, covid-19, covid19, dna, influenza, ncov, neherlab, next-generation-sequencing, nextstrain, research, rna, sars-cov-2, science, sequences, sequencing, strain, virus
- Language: TypeScript
- Homepage: https://clades.nextstrain.org
- Size: 62.6 MB
- Stars: 246
- Watchers: 16
- Forks: 65
- Open Issues: 138
- Releases: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
Owner metadata
- Name: Nextstrain
- Login: nextstrain
- Email:
- Kind: organization
- Description: Real-time tracking of pathogen evolution
- Website: https://nextstrain.org
- Location:
- Twitter: nextstrain
- Company:
- Icon url: https://avatars.githubusercontent.com/u/22159334?v=4
- Repositories: 84
- Last ynced at: 2024-04-11T18:11:56.173Z
- Profile URL: https://github.com/nextstrain
GitHub Events
Total
- Create event: 59
- Release event: 16
- Issues event: 44
- Watch event: 23
- Delete event: 10
- Issue comment event: 126
- Push event: 36
- Pull request review comment event: 7
- Pull request review event: 10
- Pull request event: 35
- Fork event: 3
Last Year
- Create event: 50
- Issues event: 41
- Release event: 15
- Watch event: 20
- Delete event: 9
- Issue comment event: 107
- Push event: 32
- Pull request review event: 9
- Pull request review comment event: 7
- Pull request event: 26
- Fork event: 3
Committers metadata
Last synced: 2 months ago
Total Commits: 5,429
Total Committers: 28
Avg Commits per committer: 193.893
Development Distribution Score (DDS): 0.161
Commits in past year: 371
Committers in past year: 5
Avg Commits per committer in past year: 74.2
Development Distribution Score (DDS) in past year: 0.102
| Name | Commits | |
|---|---|---|
| ivan-aksamentov | i****v@g****m | 4555 |
| Richard Neher | r****r@u****h | 431 |
| Cornelius Roemer | c****r@g****m | 304 |
| dependabot[bot] | 4****] | 29 |
| mt-gitlocalize | mt@g****m | 28 |
| anna-parker | a****r@g****m | 25 |
| Victor Lin | 1****n | 16 |
| Thomas Sibley | t****y@f****g | 10 |
| nextstrain-bot | n****t | 4 |
| John SJ Anderson | j****4@f****g | 3 |
| dnanto | d****2@g****u | 3 |
| snyk-bot | s****t@s****o | 3 |
| Natalie Stroud | s****1@n****u | 2 |
| Emma Hodcroft | e****t@g****m | 2 |
| Actat | a****h@g****m | 1 |
| Alex Rubinsteyn | a****n@g****m | 1 |
| Björn Grüning | b****n@g****u | 1 |
| Bryan Tegomoh | 6****h | 1 |
| Chaoran Chen | m****l@c****e | 1 |
| Christopher Bottoms | m****s | 1 |
| Finlay Maguire | f****e@g****m | 1 |
| Gordon Julian Koehn | k****g@e****h | 1 |
| John Huddleston | h****j@g****m | 1 |
| Jover Lee | j****1@g****m | 1 |
| Theo Sanderson | t****o@t****o | 1 |
| j23414 | j****g@i****u | 1 |
| Jason | J****n@m****c | 1 |
| eharkins | e****s@g****m | 1 |
Committer domains:
- fredhutch.org: 2
- iastate.edu: 1
- theo.io: 1
- ethz.ch: 1
- chaoran-chen.de: 1
- gruenings.eu: 1
- nku.edu: 1
- snyk.io: 1
- gmu.edu: 1
- gitlocalize.com: 1
- unibas.ch: 1
Issue and Pull Request metadata
Last synced: 2 months ago
Total issues: 183
Total pull requests: 516
Average time to close issues: 12 months
Average time to close pull requests: 26 days
Total issue authors: 62
Total pull request authors: 13
Average comments per issue: 2.14
Average comments per pull request: 1.49
Merged pull request: 369
Bot issues: 0
Bot pull requests: 55
Past year issues: 52
Past year pull requests: 115
Past year average time to close issues: 6 days
Past year average time to close pull requests: 6 days
Past year issue authors: 29
Past year pull request authors: 6
Past year average comments per issue: 0.98
Past year average comments per pull request: 1.03
Past year merged pull request: 76
Past year bot issues: 0
Past year bot pull requests: 19
Top Issue Authors
- corneliusroemer (53)
- ivan-aksamentov (22)
- ryhisner (7)
- ammaraziz (6)
- theosanderson (6)
- liamxg (6)
- AngieHinrichs (5)
- joverlee521 (5)
- FedeGueli (4)
- anna-parker (3)
- jameshadfield (3)
- fanninpm (3)
- rneher (3)
- victorlin (3)
- genehack (3)
Top Pull Request Authors
- ivan-aksamentov (344)
- corneliusroemer (57)
- dependabot[bot] (55)
- rneher (30)
- tsibley (11)
- victorlin (7)
- genehack (3)
- anna-parker (3)
- gordonkoehn (2)
- joverlee521 (1)
- BryanTegomoh (1)
- nodrogluap (1)
- huddlej (1)
Top Issue Labels
- t:bug (67)
- t:feat (66)
- help wanted (64)
- good first issue (61)
- needs triage (56)
- t:ask (33)
- package: nextclade_web (27)
- t:talk (8)
- package: nextclade_cli (6)
- prio: low (5)
- package: nextclade (5)
- docs (4)
- s:nextclade_web (2)
- package: nextalign (2)
- package: nextalign_cli (2)
- prio:medium (2)
- v2 (2)
- nextclade_data (2)
- v3 (1)
- os: macOS (1)
- wontfix (1)
- source: office hours (1)
Top Pull Request Labels
- dependencies (54)
- javascript (38)
- github_actions (6)
- t:bug (1)
- docs (1)
Package metadata
- Total packages: 2
-
Total downloads:
- npm: 581 last-month
- Total dependent packages: 2 (may contain duplicates)
- Total dependent repositories: 1 (may contain duplicates)
- Total versions: 58
- Total maintainers: 7
npmjs.org: @neherlab/nextclade
Nextclade version 0.x is deprecated. It means that we no longer recommend to use it. Please upgrade to the most recent version, containing latest bug fixes and new features. Make sure you remove the old version to avoid conflicts. The latest information a
- Homepage: https://clades.nextstrain.org
- Status: deprecated
- Licenses: MIT
- Latest release: 0.16.1 (published over 3 years ago)
- Last Synced: 2025-10-26T01:34:35.005Z (2 months ago)
- Versions: 50
- Dependent Packages: 1
- Dependent Repositories: 1
- Downloads: 508 Last month
-
Rankings:
- Forks count: 3.842%
- Stargazers count: 4.251%
- Dependent repos count: 10.768%
- Average: 12.527%
- Dependent packages count: 21.31%
- Downloads: 22.464%
- Maintainers (2)
npmjs.org: @nextstrain/nextclade
Nextclade version 0.x is deprecated. It means that we no longer recommend to use it. Please upgrade to the most recent version, containing latest bug fixes and new features. Make sure you remove the old version to avoid conflicts. The latest information a
- Homepage: https://clades.nextstrain.org
- Status: deprecated
- Licenses: MIT
- Latest release: 0.16.0 (published over 3 years ago)
- Last Synced: 2025-10-26T01:34:34.253Z (2 months ago)
- Versions: 8
- Dependent Packages: 1
- Dependent Repositories: 0
- Downloads: 73 Last month
-
Rankings:
- Forks count: 4.557%
- Stargazers count: 5.173%
- Dependent packages count: 16.224%
- Average: 16.58%
- Dependent repos count: 25.328%
- Downloads: 31.618%
- Maintainers (7)
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Score: 15.66466308016903