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ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis

ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis - Published in JOSS (2022)

https://github.com/norwegianveterinaryinstitute/alppaca

Science Score: 93.0%

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 9 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org, zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

clustering nextflow phylogeny pipeline
Last synced: 6 months ago · JSON representation

Repository

A tooL for Prokaryotic Phylogeny And Clustering Analysis

Basic Info
  • Host: GitHub
  • Owner: NorwegianVeterinaryInstitute
  • License: bsd-3-clause
  • Language: Nextflow
  • Default Branch: master
  • Homepage:
  • Size: 52.7 MB
Statistics
  • Stars: 12
  • Watchers: 1
  • Forks: 4
  • Open Issues: 7
  • Releases: 14
Topics
clustering nextflow phylogeny pipeline
Created over 5 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License

README.md

DOI DOI Nextflow run with conda run with docker run with singularity License

Ellipsis

Logo generated with www.biorender.com

Information

ALPPACA is a pipeline for various phylogenetic analyses of prokaryotic isolates. The pipeline includes core genome-, core gene-, and reference-based (mapping) phylogeny, as well as FastANI and cgMLST (under development). Please see the description page for more information.

Installation and Running

Please check the wiki. - Installation - How to run - Output file descriptions

Citation

ALPPACA has been published in Journal of Open Source Software. Use the following citation:

Kaspersen et al., (2022). ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis. Journal of Open Source Software, 7(79), 4677, https://doi.org/10.21105/joss.04677

Owner

  • Name: Norwegian Veterinary Institute
  • Login: NorwegianVeterinaryInstitute
  • Kind: organization

JOSS Publication

ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis
Published
November 29, 2022
DOI
Volume 7, Issue 79, Page 4677
Authors
Håkon Kaspersen ORCID
Norwegian Veterinary Institute, Ås, Norway
Eve Zeyl Fiskebeck ORCID
Norwegian Veterinary Institute, Ås, Norway
Editor
Charlotte Soneson ORCID
Tags
Phylogeny Prokaryote Clustering
View PDF Review Thread Software Archive

GitHub Events

Total
  • Create event: 2
  • Release event: 1
  • Issues event: 8
  • Watch event: 4
  • Delete event: 2
  • Issue comment event: 13
  • Push event: 8
  • Gollum event: 1
  • Pull request event: 11
Last Year
  • Create event: 2
  • Release event: 1
  • Issues event: 8
  • Watch event: 4
  • Delete event: 2
  • Issue comment event: 13
  • Push event: 8
  • Gollum event: 1
  • Pull request event: 11

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 530
  • Total Committers: 2
  • Avg Commits per committer: 265.0
  • Development Distribution Score (DDS): 0.008
Past Year
  • Commits: 5
  • Committers: 2
  • Avg Commits per committer: 2.5
  • Development Distribution Score (DDS): 0.2
Top Committers
Name Email Commits
Håkon Kaspersen h****n@v****o 526
Eve Zeyl Fiskebeck 4****l 4
Committer Domains (Top 20 + Academic)
vetinst.no: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 63
  • Total pull requests: 64
  • Average time to close issues: about 2 months
  • Average time to close pull requests: about 21 hours
  • Total issue authors: 5
  • Total pull request authors: 3
  • Average comments per issue: 1.54
  • Average comments per pull request: 0.17
  • Merged pull requests: 56
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 4
  • Pull requests: 14
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 13 minutes
  • Issue authors: 3
  • Pull request authors: 2
  • Average comments per issue: 0.75
  • Average comments per pull request: 0.29
  • Merged pull requests: 11
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • hkaspersen (40)
  • evezeyl (15)
  • solveigmo (3)
  • snogu (2)
  • rcannood (2)
Pull Request Authors
  • hkaspersen (60)
  • evezeyl (4)
  • csoneson (1)
Top Labels
Issue Labels
enhancement (29) bug (5) documentation (1)
Pull Request Labels
released (7)

Dependencies

.github/workflows/ci.yml actions
  • actions/checkout v2 composite