Nextclade

Nextclade: clade assignment, mutation calling and quality control for viral genomes - Published in JOSS (2021)

Science Score: 95.0%

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

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 6 DOI reference(s) in README and JOSS metadata
✓
Academic publication links
Links to: joss.theoj.org
✓
Committers with academic emails
5 of 28 committers (17.9%) from academic institutions
○
Institutional organization owner
✓
JOSS paper metadata
Published in Journal of Open Source Software

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

ode mesh benchmarking

Last synced: 6 months ago · JSON representation

Repository

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

Basic Info

Host: GitHub
Owner: nextstrain
License: mit
Language: Rust
Default Branch: master
Homepage: https://clades.nextstrain.org
Size: 62.7 MB

Statistics

Stars: 243
Watchers: 19
Forks: 64
Open Issues: 132
Releases: 126

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

Created over 5 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing License

Nextclade

Viral genome clade assignment, mutation calling, and sequence quality checks

by Nextstrain team

🌎 clades.nextstrain.org

| | |----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| | Brief demonstration of Nextclade Web. Large version is here. |

📜️ Citation

If you use results obtained with Nextclade in a publication, please

cite our paper:

Aksamentov, I., Roemer, C., Hodcroft, E. B., & Neher, R. A., (2021). Nextclade: clade assignment, mutation calling and quality control for viral genomes. Journal of Open Source Software, 6(67), 3773, https://doi.org/10.21105/joss.03773

(bibtex)

where possible, provide a link to Nextclade Web:

https://clades.nextstrain.org

📗 Documentation

Documentation for Nextclade: https://docs.nextstrain.org/projects/nextclade
Documentation for the parent project, Nextstrain: https://docs.nextstrain.org

🧑‍💻 Development

Read developer guide here: docs/dev/developer-guide.md

✨ Team

Nextclade is a part of Nextstrain project .

It is maintained by:

Ivan Aksamentov

Senior Software Engineer
NeherLab, Biozentrum, University of Basel
Swiss Institute of Bioinformatics

Richard Neher

Principal Investigator
NeherLab, Biozentrum, University of Basel
Swiss Institute of Bioinformatics

Cornelius Roemer

Staff Scientist
NeherLab, Biozentrum, University of Basel
Swiss Institute of Bioinformatics

We are thankful to all our contributors, no matter how they contribute: in ideas, science, code, documentation or otherwise. Thanks goes to these people (emoji key):

_{Emma Hodcroft} 🤔 ⚠️ 📢 👀	_{Anna Parker} 💻 ⚠️ 🤔	_{Thomas Sibley} 🚇 🛡️	_{Victor Lin} 💻 📖	_{Theo Sanderson} 💻	_{Natalie Stroud} 🖋 🌍	_{Alex Rubinsteyn} 📖	_{Christopher Bottoms} 📖
_{Finlay Maguire} 📖	_dnanto 💻 🔣

This project follows the all-contributors specification. Contributions of any kind welcome!

⚖️ License

MIT License

Owner

Name: Nextstrain
Login: nextstrain
Kind: organization

Website: https://nextstrain.org
Twitter: nextstrain
Repositories: 84
Profile: https://github.com/nextstrain

Real-time tracking of pathogen evolution

JOSS Publication

Nextclade: clade assignment, mutation calling and quality control for viral genomes

Published

November 30, 2021

DOI

10.21105/joss.03773

Volume 6, Issue 67, Page 3773

Authors

Ivan Aksamentov

Biozentrum, University of Basel, Switzerland, Swiss Institute of Bioinformatics, Basel, Switzerland

Cornelius Roemer

Biozentrum, University of Basel, Switzerland, Swiss Institute of Bioinformatics, Basel, Switzerland

Emma B. Hodcroft

Swiss Institute of Bioinformatics, Basel, Switzerland, Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland

Richard A. Neher

Biozentrum, University of Basel, Switzerland, Swiss Institute of Bioinformatics, Basel, Switzerland

Editor

Kelly Rowland

GitHub Events

Total

Create event: 59
Release event: 16
Issues event: 41
Watch event: 22
Delete event: 9
Issue comment event: 119
Push event: 36
Pull request review comment event: 6
Pull request review event: 10
Pull request event: 33
Fork event: 3

Last Year

Create event: 59
Release event: 16
Issues event: 41
Watch event: 22
Delete event: 9
Issue comment event: 120
Push event: 36
Pull request review comment event: 6
Pull request review event: 10
Pull request event: 33
Fork event: 3

Committers

Last synced: 7 months ago

All Time

Total Commits: 5,375
Total Committers: 28
Avg Commits per committer: 191.964
Development Distribution Score (DDS): 0.162

Past Year

Commits: 340
Committers: 7
Avg Commits per committer: 48.571
Development Distribution Score (DDS): 0.144

Top Committers

Name	Email	Commits
ivan-aksamentov	i**v@g**m	4,503
Richard Neher	r**r@u**h	431
Cornelius Roemer	c**r@g**m	304
mt-gitlocalize	mt@g****m	28
dependabot[bot]	4****]	27
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 (Top 20 + Academic)

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

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 176
Total pull requests: 500
Average time to close issues: 12 months
Average time to close pull requests: 27 days
Total issue authors: 58
Total pull request authors: 13
Average comments per issue: 2.16
Average comments per pull request: 1.51
Merged pull requests: 356
Bot issues: 0
Bot pull requests: 51

Past Year

Issues: 53
Pull requests: 123
Average time to close issues: 7 days
Average time to close pull requests: 6 days
Issue authors: 30
Pull request authors: 8
Average comments per issue: 0.89
Average comments per pull request: 1.44
Merged pull requests: 75
Bot issues: 0
Bot pull requests: 20

View more stats

Top Authors

Issue Authors

corneliusroemer (52)
ivan-aksamentov (22)
ryhisner (7)
liamxg (6)
ammaraziz (5)
theosanderson (5)
AngieHinrichs (5)
joverlee521 (5)
FedeGueli (4)
jameshadfield (3)
anna-parker (3)
fanninpm (3)
victorlin (3)
rneher (3)
genehack (3)

Pull Request Authors

ivan-aksamentov (332)
corneliusroemer (57)
dependabot[bot] (51)
rneher (30)
tsibley (11)
victorlin (7)
genehack (3)
anna-parker (3)
gordonkoehn (2)
joverlee521 (1)
BryanTegomoh (1)
nodrogluap (1)
huddlej (1)

Top Labels

Issue Labels

t:bug (66) help wanted (63) t:feat (63) good first issue (60) needs triage (53) t:ask (31) package: nextclade_web (27) t:talk (8) package: nextclade_cli (6) prio: low (5) package: nextclade (5) docs (3) package: nextalign (2) package: nextalign_cli (2) prio:medium (2) v2 (2) nextclade_data (2) v3 (1) os: macOS (1) wontfix (1) s:nextclade_web (1) source: office hours (1)

Pull Request Labels

dependencies (50) javascript (34) github_actions (6) t:bug (1) docs (1)

Packages

Total packages: 2
Total downloads:
- npm 152 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
License: MIT
Status: deprecated
Latest release: 0.16.1
published almost 4 years ago

Versions: 50
Dependent Packages: 1
Dependent Repositories: 1
Downloads: 140 Last month

Rankings

Forks count: 3.8%

Stargazers count: 4.3%

Dependent repos count: 10.8%

Average: 12.5%

Dependent packages count: 21.3%

Downloads: 22.5%

Maintainers (2)

ivan-aksamentov rneher

Last synced: 6 months ago

npmjs.org: @nextstrain/nextclade

Homepage: https://clades.nextstrain.org
License: MIT
Status: deprecated
Latest release: 0.16.0
published almost 4 years ago

Versions: 8
Dependent Packages: 1
Dependent Repositories: 0
Downloads: 12 Last month

Rankings

Forks count: 4.6%

Stargazers count: 5.2%

Dependent packages count: 16.2%

Average: 16.6%

Dependent repos count: 25.3%

Downloads: 31.6%

Maintainers (7)

jameshadfield genehack ivan-aksamentov rneher joverlee nextstrain-bot victorlin

Last synced: 6 months ago

Dependencies

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packages/nextclade-web/yarn.lock npm

2298 dependencies

docs/environment.yml conda

make
pip
recommonmark
requests
sphinx

Nextclade

Science Score: 95.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Nextclade

Viral genome clade assignment, mutation calling, and sequence quality checks

📜️ Citation

📗 Documentation

🧑‍💻 Development

✨ Team

⚖️ License

Owner

JOSS Publication

Nextclade: clade assignment, mutation calling and quality control for viral genomes

Authors

Editor

Tags

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

npmjs.org: @neherlab/nextclade

Rankings

Maintainers (2)

npmjs.org: @nextstrain/nextclade

Rankings

Maintainers (7)

Dependencies