singlem 0.20.3
Novelty-inclusive microbial community profiling of shotgun metagenomes
Requires Python: >=3.7
Keywords: metagenomics, bioinformatics



<!-- NOTE: This intro should manually be kept in sync between the repo README and the docs README -->

[![Sandpiper logo](./docs/_include/sandpiper_small.png)](https://sandpiper.qut.edu.au)
[![Bin Chicken logo](./docs/_include/binchicken_small.png)](https://aroneys.github.io/binchicken)
[![Lyrebird logo](./docs/_include/lyrebird_small.png)](/Lyrebird)


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Welcome.

At heart, SingleM is a tool for profiling shotgun (both short and long-read) metagenomes. It [shows](https://doi.org/10.1101/2024.01.30.578060) 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](https://sandpiper.qut.edu.au).

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](https://wwood.github.io/singlem/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](https://aroneys.github.io/binchicken/)).

Documentation can be found at https://wwood.github.io/singlem/.

## Citations
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### 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](https://doi.org/10.1038/s41587-025-02738-1).
### SingleM prokaryotic_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](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](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).