Welcome.

SingleM is a tool for profiling shotgun metagenomes. It has a particular strength in detecting microbial lineages which are not in reference databases. The method it uses also makes it suitable for some related tasks, such as assessing eukaryotic contamination, finding bias in genome recovery, computing ecological diversity metrics, and lineage-targeted MAG recovery.

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

SingleM and Sandpiper: Robust microbial taxonomic profiles from metagenomic data. Ben J Woodcroft, Samuel T. N. Aroney, Rossen Zhao, Mitchell Cunningham, Joshua A. M. Mitchell, Linda Blackall, Gene W Tyson. bioRxiv 2024.01.30.578060; doi: https://doi.org/10.1101/2024.01.30.578060