https://github.com/aroneys/singlem
De-novo OTUs from shotgun metagenomes
Science Score: 13.0%
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Found 14 DOI reference(s) in README -
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Low similarity (6.1%) to scientific vocabulary
Repository
De-novo OTUs from shotgun metagenomes
Basic Info
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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: Samuel Aroney
- Login: AroneyS
- Kind: user
- Website: https://aroneys.github.io/
- Twitter: aroney_samuel
- Repositories: 11
- Profile: https://github.com/AroneyS
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Last Year
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Dependencies
- actions-rs/toolchain v1.0.6 composite
- actions/checkout v3 composite
- crazy-max/ghaction-github-pages v3.0.0 composite
- actions/checkout v3 composite
- conda-incubator/setup-miniconda v2.2.0 composite
- actions/checkout v2 composite
- actions/setup-python v2 composite
- casperdcl/deploy-pypi v2 composite