ont-bacpac-nf
Bacterial profiling workflow for ONT data, written in Nextflow.
Science Score: 65.0%
This score indicates how likely this project is to be science-related based on various indicators:
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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 2 DOI reference(s) in README -
○Academic publication links
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○Academic email domains
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✓Institutional organization owner
Organization sydney-informatics-hub has institutional domain (sydney.edu.au) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.0%) to scientific vocabulary
Repository
Bacterial profiling workflow for ONT data, written in Nextflow.
Basic Info
Statistics
- Stars: 2
- Watchers: 6
- Forks: 0
- Open Issues: 24
- Releases: 0
Metadata Files
README.md
ONT-bacpac-nf
Workflow description
A rapid and portable workflow for pond-side sequencing of bacterial pathogens for sustainable aquaculture using ONT long-read sequencing.
User guide
See the following docs: - Getting started: docs/getting-started.md - Gadi execution: docs/gadi-execution.md - Interpreting results: docs/interpreting-results.md - Developer instructions: docs/developers.md
Component tools
Coming soon
Additional notes
Coming soon
Help / FAQ / Troubleshooting
Please submit an issue for any bug reports, feature requests, or questions.
Acknowledgements/citations/credits
Acknowledgements (and co-authorship, where appropriate) are an important way for us to demonstrate the value we bring to your research. Your research outcomes are vital for ongoing funding of the Sydney Informatics Hub and national compute facilities.
Authors
- Francisca Samsing (Sydney School of Veterinary Science, University of Sydney)
- Georgie Samaha (Sydney Informatics Hub, University of Sydney)
- Michael Geaghan (Sydney Informatics Hub, University of Sydney)
- Fred Jaya (Sydney Informatics Hub, University of Sydney)
- Mitchell O'Brien (Sydney Informatics Hub, University of Sydney)
Suggested acknowledgement
The authors acknowledge the support provided by the Sydney Informatics Hub, a Core Research Facility of the University of Sydney. This research/project was undertaken with the assistance of resources and services from the National Computational Infrastructure (NCI), which is supported by the Australian Government, and the Australian BioCommons which is enabled by NCRIS via Bioplatforms Australia funding.
Cite us to support us!
You can cite this pipeline as:
Samaha, G., Samsing, F., O'Brien, M., Jaya, F. & Geaghan, M. (2025). ONT-bacpac-nf (Version 1.0.0) [Computer software]. https://doi.org/10.48546/workflowhub.workflow.1263.1
Owner
- Name: Sydney Informatics Hub
- Login: Sydney-Informatics-Hub
- Kind: organization
- Email: sih.admin@sydney.edu.au
- Location: University of Sydney, Sydney Australia
- Website: https://sydney.edu.au/sydney-informatics-hub
- Twitter: Sydney_CRF
- Repositories: 189
- Profile: https://github.com/Sydney-Informatics-Hub
The Sydney Informatics Hub is a Core Research Facility of the University of Sydney, providing training and expertise on research data, analysis and computing.
Citation (CITATION.cff)
cff-version: 1.0.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Samaha"
given-names: "Georgina"
orcid: "https://orcid.org/0000-0003-0419-1476"
- family-names: "Samsing"
given-names: "Francisca"
orcid: "https://orcid.org/0000-0002-6343-2295"
- family-names: "O'Brien"
given-names: "Mitchell"
orcid: "https://orcid.org/0000-0003-0662-9101"
- family-names: "Jaya"
given-names: "Frederick"
orcid: "https://orcid.org/0000-0002-4019-7026"
title: "ONT-bacpac-nf"
version: 1.0.0
doi: 10.48546/workflowhub.workflow.1263.1
date-released: 2025-01-31
url: "https://github.com/Sydney-Informatics-Hub/ONT-bacpac-nf"
GitHub Events
Total
- Issues event: 40
- Watch event: 1
- Delete event: 12
- Issue comment event: 35
- Push event: 76
- Pull request review event: 15
- Pull request review comment event: 3
- Pull request event: 27
- Create event: 20
Last Year
- Issues event: 40
- Watch event: 1
- Delete event: 12
- Issue comment event: 35
- Push event: 76
- Pull request review event: 15
- Pull request review comment event: 3
- Pull request event: 27
- Create event: 20
Issues and Pull Requests
Last synced: 8 months ago
All Time
- Total issues: 60
- Total pull requests: 48
- Average time to close issues: about 2 months
- Average time to close pull requests: 6 days
- Total issue authors: 7
- Total pull request authors: 6
- Average comments per issue: 0.65
- Average comments per pull request: 0.81
- Merged pull requests: 38
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 28
- Pull requests: 33
- Average time to close issues: about 2 months
- Average time to close pull requests: 5 days
- Issue authors: 6
- Pull request authors: 4
- Average comments per issue: 0.71
- Average comments per pull request: 0.64
- Merged pull requests: 25
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- georgiesamaha (40)
- mgeaghan (9)
- fredjaya (7)
- fransamsing (2)
- nandan75 (2)
- laclac102 (1)
- Mitchob (1)
Pull Request Authors
- georgiesamaha (24)
- mgeaghan (16)
- nandan75 (9)
- fredjaya (7)
- gdmcdonald (6)
- Mitchob (2)