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autocycler

A tool for generating consensus long-read assemblies for bacterial genomes

https://github.com/rrwick/autocycler

Science Score: 67.0%

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

  • ✓
    CITATION.cff file
    Found 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
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.5%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

A tool for generating consensus long-read assemblies for bacterial genomes

Basic Info
  • Host: GitHub
  • Owner: rrwick
  • License: gpl-3.0
  • Language: Rust
  • Default Branch: main
  • Homepage:
  • Size: 1.08 MB
Statistics
  • Stars: 174
  • Watchers: 1
  • Forks: 15
  • Open Issues: 0
  • Releases: 10
Created over 2 years ago · Last pushed 6 months ago
Metadata Files
Readme License Citation

README.md

Autocycler logo

License GPL v3 Rust DOI

Autocycler is a tool for generating consensus long-read assemblies for bacterial genomes. It is the successor to Trycycler, and for most users, I recommend Autocycler over Trycycler.

For installation instructions, usage, deeper explanations and more, head over to the Autocycler wiki!

If you use Autocycler in your research, please cite the following paper:
Wick RR, Howden BP, Stinear TP (2025). Autocycler: long-read consensus assembly for bacterial genomes. Bioinformatics. doi:10.1093/bioinformatics/btaf474.

Owner

  • Name: Ryan Wick
  • Login: rrwick
  • Kind: user
  • Location: Melbourne, Australia
  • Company: University of Melbourne

I'm a bioinformatician with a focus on bacterial genome assembly.

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite the associated preprint listed below."
title: "Autocycler"
authors:
  - family-names: "Wick"
    given-names: "Ryan R"
    orcid: "https://orcid.org/0000-0001-8349-0778"
url: "https://github.com/rrwick/Autocycler"
preferred-citation:
  type: article
  authors:
    - family-names: "Wick"
      given-names: "Ryan R"
      orcid: "https://orcid.org/0000-0001-8349-0778"
    - family-names: "Howden"
      given-names: "Benjamin P"
      orcid: "https://orcid.org/0000-0003-0237-1473"
    - family-names: "Stinear"
      given-names: "Timothy P"
      orcid: "https://orcid.org/0000-0003-0150-123X"
  title: "Autocycler: long-read consensus assembly for bacterial genomes"
  journal: "bioRxiv"
  year: 2025
  month: 5
  doi: "10.1101/2025.05.12.653612"

GitHub Events

Total
  • Create event: 6
  • Release event: 6
  • Issues event: 52
  • Watch event: 153
  • Delete event: 1
  • Issue comment event: 72
  • Public event: 1
  • Push event: 76
  • Pull request event: 19
  • Gollum event: 126
  • Fork event: 17
Last Year
  • Create event: 6
  • Release event: 6
  • Issues event: 52
  • Watch event: 153
  • Delete event: 1
  • Issue comment event: 72
  • Public event: 1
  • Push event: 76
  • Pull request event: 19
  • Gollum event: 126
  • Fork event: 17

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 32
  • Total pull requests: 11
  • Average time to close issues: 2 days
  • Average time to close pull requests: 1 day
  • Total issue authors: 28
  • Total pull request authors: 9
  • Average comments per issue: 0.91
  • Average comments per pull request: 0.36
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 32
  • Pull requests: 11
  • Average time to close issues: 2 days
  • Average time to close pull requests: 1 day
  • Issue authors: 28
  • Pull request authors: 9
  • Average comments per issue: 0.91
  • Average comments per pull request: 0.36
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • hkaspersen (3)
  • padpadpadpad (2)
  • DBrache (2)
  • samlipworth (1)
  • tomdstanton (1)
  • xiaoli-dong (1)
  • RicardoGCCR (1)
  • muntean-alex (1)
  • ak-watson (1)
  • Tux-2003 (1)
  • stevebaeyen (1)
  • ericvdtoorn (1)
  • ankane (1)
  • EricDeveaud (1)
  • SJSalter (1)
Pull Request Authors
  • tomdstanton (2)
  • MrTomRod (2)
  • yvlaere (1)
  • Cmnorris7 (1)
  • rrwick (1)
  • HForrest (1)
  • iskold (1)
  • ericvdtoorn (1)
  • ppenev-eligo (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • homebrew 33 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 4
formulae.brew.sh: autocycler

Tool for generating consensus long-read assemblies for bacterial genomes

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 33 Last month
Rankings
Dependent packages count: 16.4%
Average: 41.2%
Dependent repos count: 48.0%
Downloads: 59.1%
Last synced: 6 months ago

Dependencies

.github/workflows/rust.yml actions
  • actions/checkout v4 composite
Cargo.lock cargo
  • 210 dependencies
Cargo.toml cargo
scripts/Dockerfile docker
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scripts/environment.yml pypi