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).
The main idea of SingleM is to profile metagenomes by targeting short 20 amino acid stretches ("windows") within single copy marker genes. It finds reads which cover an entire window, and analyses these further. By constraining analysis to these short windows, it becomes possible to know how novel each read is compared to known genomes. Then, using the fact that each analysed gene is (almost always) found exactly once in each genome, the abundance of each lineage can be accurately estimated.
There are several tools (subcommands) which can be used after installation:
- singlem pipe - the main workflow which generates OTU tables and GTDB taxonomic profiles.
- single summarise - Mechanical transformations of
singlem piperesults. - singlem renew - Given previously generated results, re-run the pipeline with a new reference sequence/taxonomy database.
- singlem supplement - Add new genomes to a reference metapackage.
- singlem prokaryotic_fraction - How much of a metagenome is prokaryotic? (also available as
microbial_fraction, the deprecated name) - singlem appraise - How much of a metagenome do the genomes or assembly represent?
And more specialised / expert modes:
- singlem condense - Given an OTU table, summarise the results into a taxonomic profile.
- singlem makedb & query- Create a database of OTU sequences and query it using various sequence similarity methods e.g. smafa.
Help
If you have any questions or comments, raise a GitHib issue or just send us an email.
License
SingleM is developed by the Woodcroft lab at the Centre for Microbiome Research, School of Biomedical Sciences, QUT, with contributions from many helpful people including Samuel Aroney, Rossen Zhao, and Raphael Eisenhofer. It is licensed under GPL3 or later.
The source code is available at https://github.com/wwood/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, 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).
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