trycycler
A tool for generating consensus long-read assemblies for bacterial genomes
Science Score: 67.0%
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✓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
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (5.4%) to scientific vocabulary
Repository
A tool for generating consensus long-read assemblies for bacterial genomes
Basic Info
Statistics
- Stars: 318
- Watchers: 13
- Forks: 29
- Open Issues: 3
- Releases: 15
Metadata Files
README.md
Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes. I.e. if you have multiple long-read assemblies for the same isolate, Trycycler can combine them into a single assembly that is better than any of your inputs.
For installation instructions, usage, deeper explanations and more, head over to the Trycycler wiki!
For our paper describing Trycycler, follow this link: Wick RR, Judd LM, Cerdeira LT, Hawkey J, Méric G, Vezina B, Wyres KL, Holt KE. Trycycler: consensus long-read assemblies for bacterial genomes. Genome Biology. 2021. doi:10.1186/s13059-021-02483-z.
Owner
- Name: Ryan Wick
- Login: rrwick
- Kind: user
- Location: Melbourne, Australia
- Company: University of Melbourne
- Website: https://rrwick.github.io
- Twitter: rrwick
- Repositories: 24
- Profile: https://github.com/rrwick
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 it as below."
authors:
- family-names: "Wick"
given-names: "Ryan R"
orcid: "https://orcid.org/0000-0001-8349-0778"
title: "Trycycler"
url: "https://github.com/rrwick/Trycycler"
preferred-citation:
type: article
authors:
- family-names: "Wick"
given-names: "Ryan R"
orcid: "https://orcid.org/0000-0001-8349-0778"
- family-names: "Judd"
given-names: "Louise M"
- family-names: "Cerdeira"
given-names: "Louise T"
- family-names: "Hawkey"
given-names: "Jane"
- family-names: "Méric"
given-names: "Guillaume"
- family-names: "Vezina"
given-names: "Ben"
- family-names: "Wyres"
given-names: "Kelly L"
- family-names: "Holt"
given-names: "Kathryn E"
doi: "10.1186/s13059-021-02483-z"
journal: "Genome Biology"
month: 9
title: "Trycycler: consensus long-read assemblies for bacterial genomes"
volume: 22
year: 2021
GitHub Events
Total
- Issues event: 13
- Watch event: 20
- Issue comment event: 27
- Pull request event: 1
- Gollum event: 4
- Fork event: 2
Last Year
- Issues event: 13
- Watch event: 20
- Issue comment event: 27
- Pull request event: 1
- Gollum event: 4
- Fork event: 2
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 5
- Total pull requests: 1
- Average time to close issues: about 1 month
- Average time to close pull requests: 5 days
- Total issue authors: 5
- Total pull request authors: 1
- Average comments per issue: 1.6
- Average comments per pull request: 1.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 5
- Pull requests: 1
- Average time to close issues: about 1 month
- Average time to close pull requests: 5 days
- Issue authors: 5
- Pull request authors: 1
- Average comments per issue: 1.6
- Average comments per pull request: 1.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- DingJingZhi (2)
- niederhuth (1)
- fergsc (1)
- georgiesamaha (1)
- zmqstc (1)
- francescodc87 (1)
- aharring83 (1)
- abcdot (1)
- mesti90 (1)
- osvatic (1)
- sghignone (1)
- TobyHelol (1)
- erikwolfsohn (1)
- muntean-alex (1)
- ASUQ (1)
Pull Request Authors
- anaome (1)
- ASUQ (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- edlib *
- numpy *
- pillow *
- pytest *
- scipy *
- edlib *
- numpy *
- pillow *
- pytest *
- scipy *