Welcome.
At heart, SingleM is a tool for profiling shotgun (both short and long-read) metagenomes. It shows good accuracy in estimating the relative abundances of community members, and has a particular strength in dealing with novel lineages.
It was originally designed to determine the relative abundance of bacterial and archaeal taxa in a sample. Microbial SingleM has been applied to ~700,000 public metagenomes. The resulting data are available at the Sandpiper companion website.
Recent versions have added features:
- Long-read input support (v0.20.0). Either Nanopore >= R10.4.1 or PacBio HiFi reads are recommended to ensure reliable taxonomic profiling.
- Profiling of dsDNA phages (v0.19.0, updated DB in v0.20.0). See Lyrebird.
The method it uses also 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).
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 prokaryotic_fraction
Raphael Eisenhofer, Antton Alberdi, Ben J. Woodcroft. Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns. mSystems 0:e01062-25 (2026). https://doi.org/10.1128/msystems.01062-25.
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. Nat Methods 22, 2516–2524 (2025). https://doi.org/10.1038/s41592-025-02901-1
Lyrebird
Rossen Zhao, Gene W. Tyson, Ben J. Woodcroft. Lyrebird: a tool for profiling dsDNA phage communities in metagenomic data. (in preparation).
Release files for singlem 0.21.4
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| singlem-0.21.4.tar.gz | 1.6 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| singlem-0.21.4-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 1.9 MB
Release files / singlem-0.21.4.tar.gz
| Download URL | singlem-0.21.4.tar.gz |
|---|---|
| Size | 1.6 MB |
| Tags | Source |
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SHA-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.14.7
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Release files / singlem-0.21.4-py3-none-any.whl
| Download URL | singlem-0.21.4-py3-none-any.whl |
|---|---|
| Size | 228.8 kB |
| Tags | Python 3 |
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SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.14.7
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