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amptk

AMPtk: Amplicon ToolKit for NGS data (formally UFITS)

https://github.com/nextgenusfs/amptk

Science Score: 33.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    2 of 14 committers (14.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (2.6%) to scientific vocabulary

Keywords

amplicons co1 coi fungi lsu microbiome mtco1 mycobiome next-generation-sequencing rdna

Keywords from Contributors

genome-annotation comparative-genomics gene-models ncbi-submission bioinformatics taxonomic-classification genomics
Last synced: 6 months ago · JSON representation

Repository

AMPtk: Amplicon ToolKit for NGS data (formally UFITS)

Basic Info
  • Host: GitHub
  • Owner: nextgenusfs
  • License: bsd-2-clause
  • Language: Python
  • Default Branch: master
  • Homepage: http://amptk.readthedocs.io/
  • Size: 18.3 MB
Statistics
  • Stars: 38
  • Watchers: 8
  • Forks: 14
  • Open Issues: 14
  • Releases: 83
Topics
amplicons co1 coi fungi lsu microbiome mtco1 mycobiome next-generation-sequencing rdna
Created over 10 years ago · Last pushed over 2 years ago
Metadata Files
Readme License

README.md

DOI Conda

AMPtk

NGS AMPlicon Tool Kit:

Documentation: http://amptk.readthedocs.io/

Citation

Palmer JM, Jusino MA, Banik MT, Lindner DL. 2018. Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data. PeerJ 6:e4925; DOI 10.7717/peerj.4925.

https://peerj.com/articles/4925/

Owner

  • Name: Jon Palmer
  • Login: nextgenusfs
  • Kind: user
  • Location: Palo Alto, CA

GitHub Events

Total
  • Issues event: 1
Last Year
  • Issues event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 632
  • Total Committers: 14
  • Avg Commits per committer: 45.143
  • Development Distribution Score (DDS): 0.343
Past Year
  • Commits: 2
  • Committers: 1
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Jon Palmer j****n@J****l 415
Jon Palmer n****s@g****m 144
Jon Palmer n****s@g****m 45
Jon Palmer j****n@J****t 10
Ion PGM n****s@n****s 4
Jon Palmer j****n@c****u 3
Jason Stajich j****d@g****m 3
Jason Stajich j****h@u****u 2
CFMR NGS n****s@C****l 1
Jason Stajich j****h@g****m 1
Andreas Sjödin a****n@g****m 1
strund3r f****r@g****m 1
Jon Palmer j****n@J****n 1
Vladimir Mikryukov v****k 1
Committer Domains (Top 20 + Academic)
jons-mbp.lan: 1 ucr.edu: 1 calvisitor-10-105-185-148.calvisitor.1918.berkeley.edu: 1 ngs-mac-pro.fpl.fs.fed.us: 1 jons-mbp.attlocal.net: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 93
  • Total pull requests: 12
  • Average time to close issues: 4 months
  • Average time to close pull requests: 15 days
  • Total issue authors: 35
  • Total pull request authors: 5
  • Average comments per issue: 4.03
  • Average comments per pull request: 0.5
  • Merged pull requests: 11
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • nextgenusfs (13)
  • devonorourke (10)
  • peterjc (9)
  • MycoMap (8)
  • vmikk (6)
  • JonathanVanHamme (5)
  • bsmoda (5)
  • hyphaltip (3)
  • Alenap26 (3)
  • hlfreund (2)
  • nicolereynolds1 (2)
  • atiweb (2)
  • yuanyuan12543 (2)
  • FilipeMatteoli (2)
  • cour10eygrace (1)
Pull Request Authors
  • hyphaltip (7)
  • nextgenusfs (2)
  • druvus (1)
  • vmikk (1)
  • strund3r (1)
Top Labels
Issue Labels
enhancement (9) bug (3) question (2)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 99 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 11
  • Total maintainers: 1
pypi.org: amptk

AMPtk: amplicon tool kit

  • Versions: 11
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 99 Last month
  • Docker Downloads: 0
Rankings
Docker downloads count: 4.2%
Forks count: 9.6%
Dependent packages count: 10.0%
Stargazers count: 10.9%
Average: 11.8%
Downloads: 14.6%
Dependent repos count: 21.7%
Maintainers (1)
nextgenusfs
Last synced: 6 months ago

Dependencies

.github/workflows/main.yml actions
  • actions/checkout v2 composite
  • docker/build-push-action v2 composite
  • docker/login-action v1 composite
  • docker/setup-buildx-action v1 composite
  • peter-evans/repository-dispatch v1 composite
.github/workflows/python-publish.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/release-triggered.yml actions
  • actions/checkout v2 composite
  • docker/build-push-action v2 composite
  • docker/login-action v1 composite
  • docker/setup-buildx-action v1 composite
  • kaliber5/action-get-release v1 composite
.github/workflows/release.yml actions
  • actions/checkout v2 composite
  • docker/build-push-action v2 composite
  • docker/login-action v1 composite
  • docker/setup-buildx-action v1 composite
  • kaliber5/action-get-release v1 composite
  • peter-evans/repository-dispatch v1 composite
.github/workflows/triggered-build.yml actions
  • actions/checkout v2 composite
  • docker/build-push-action v2 composite
  • docker/login-action v1 composite
  • docker/setup-buildx-action v1 composite
Dockerfile docker
  • continuumio/miniconda3 latest build
  • debian buster build