singlem 0.21.3

Novelty-inclusive microbial community profiling of shotgun metagenomes

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).