singlem
Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes
Science Score: 49.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 14 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
5 of 11 committers (45.5%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (6.5%) to scientific vocabulary
Keywords
Repository
Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes
Basic Info
- Host: GitHub
- Owner: wwood
- License: gpl-3.0
- Language: Python
- Default Branch: main
- Homepage: http://wwood.github.io/singlem/
- Size: 305 MB
Statistics
- Stars: 161
- Watchers: 8
- Forks: 20
- Open Issues: 41
- Releases: 0
Topics
Metadata Files
README.md
Welcome.
At heart, SingleM is a tool for profiling shotgun metagenomes. It was originally designed to determine the relative abundance of bacterial and archaeal taxa in a sample. As of version 0.19.0, it can also be used to profile dsDNA phages (see Lyrebird).
It shows good accuracy in estimating the relative abundances of community members, and has a particular strength in dealing with novel lineages. The method it uses also makes it suitable for some related tasks, such as assessing eukaryotic contamination, finding bias in genome recovery, and lineage-targeted MAG recovery. It can also be used as the basis for choosing metagenomes which, when coassembled, maximise the recovery of novel MAGs (see Bin Chicken).
Microbial SingleM has been applied to ~700,000 public metagenomes. The resulting data are available at the Sandpiper companion website.
Documentation can be found at https://wwood.github.io/singlem/
Citations
Profiling microbial communities with SingleM / Sandpiper
Ben J. Woodcroft, Samuel T. N. Aroney, Rossen Zhao, Mitchell Cunningham, Joshua A. M. Mitchell, Rizky Nurdiansyah, Linda Blackall & Gene W. Tyson. Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper. Nat Biotechnol (2025). https://doi.org/10.1038/s41587-025-02738-1.
SingleM microbial_fraction
Raphael Eisenhofer, Antton Alberdi, Ben J. Woodcroft, 2024. Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns. bioRxiv, pp.2024-05; https://doi.org/10.1101/2024.05.16.594470.
SingleM-powered coassembly with Bin Chicken
Samuel T. N. Aroney, Rhys J. Newell, Gene W. Tyson and Ben J. Woodcroft, 2024. Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes. bioRxiv, pp.2024-11. https://doi.org/10.1101/2024.11.24.625082.
Lyrebird
Rossen Zhao, Gene W. Tyson, Ben J. Woodcroft. Lyrebird: a tool for profiling dsDNA phage communities in metagenomic data. (in preparation).
Owner
- Name: Ben J Woodcroft
- Login: wwood
- Kind: user
- Location: Brisbane, University of Queensland
- Company: Queensland University of Technology
- Website: https://research.qut.edu.au/cmr/team/ben-woodcroft
- Twitter: wwood
- Repositories: 202
- Profile: https://github.com/wwood
Informatics team leader at the Centre for Microbiome Research (CMR)
GitHub Events
Total
- Create event: 16
- Release event: 1
- Issues event: 30
- Watch event: 20
- Delete event: 6
- Member event: 1
- Issue comment event: 107
- Push event: 84
- Pull request review event: 32
- Pull request review comment event: 47
- Pull request event: 46
- Fork event: 3
Last Year
- Create event: 16
- Release event: 1
- Issues event: 30
- Watch event: 20
- Delete event: 6
- Member event: 1
- Issue comment event: 107
- Push event: 84
- Pull request review event: 32
- Pull request review comment event: 47
- Pull request event: 46
- Fork event: 3
Committers
Last synced: 10 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Ben Woodcroft | d****n@g****m | 1,183 |
| AroneyS | s****y@q****u | 142 |
| Ben J. Woodcroft | d****m | 107 |
| rzhao-2 | r****o@g****m | 31 |
| EisenRa | r****r@g****m | 3 |
| thepatientwait | 9****t | 1 |
| Aaron Mussig | a****g@g****m | 1 |
| rzhao-2 | s****5@m****u | 1 |
| rzhao-2 | s****5@d****u | 1 |
| Tim Lamberton | t****n@u****u | 1 |
| Rossen Zhao | z****3@c****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 122
- Total pull requests: 112
- Average time to close issues: 3 months
- Average time to close pull requests: 17 days
- Total issue authors: 82
- Total pull request authors: 6
- Average comments per issue: 2.75
- Average comments per pull request: 1.15
- Merged pull requests: 85
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 25
- Pull requests: 44
- Average time to close issues: 3 days
- Average time to close pull requests: 8 days
- Issue authors: 22
- Pull request authors: 4
- Average comments per issue: 1.32
- Average comments per pull request: 1.25
- Merged pull requests: 29
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- adityabandla (9)
- LiZhihua1982 (3)
- slambrechts (3)
- rzhao-2 (3)
- rachaellappan (3)
- pm-leung (3)
- lauramason326 (3)
- michoug (3)
- wwood (3)
- xvazquezc (2)
- ellyyuyang (2)
- Valentin-Bio (2)
- julianzaugg (2)
- kjvilardi (2)
- Ge0rges (2)
Pull Request Authors
- AroneyS (47)
- rzhao-2 (44)
- wwood (12)
- thepatientwait (6)
- EisenRa (2)
- aaronmussig (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 113 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 22
- Total maintainers: 2
pypi.org: singlem
Novelty-inclusive microbial community profiling of shotgun metagenomes
- Homepage: https://github.com/wwood/SingleM
- Documentation: https://singlem.readthedocs.io/
- License: gpl-3.0
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Latest release: 0.19.0
published 10 months ago