Skip to main content

Novelty-inclusive microbial community profiling of shotgun metagenomes

Project description

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, and lineage-targeted MAG recovery.

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

Community profiles for many publicly available metagenomes can be found at the Sandpiper website.

Citations

The overall citation for SingleM/Sandpiper:

Woodcroft, Ben J., Samuel TN Aroney, Rossen Zhao, Mitchell Cunningham, Joshua AM Mitchell, Linda Blackall, and Gene W. Tyson. SingleM and Sandpiper: Robust microbial taxonomic profiles from metagenomic data. bioRxiv (2024): 2024-01. https://doi.org/10.1101/2024.01.30.578060

The microbial_fraction (SMF) mode of SingleM:

Eisenhofer, Raphael, Antton Alberdi, and Ben J. Woodcroft. Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns. bioRxiv (2024): 2024-05. https://doi.org/10.1101/2024.05.16.594470

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

singlem-0.18.3.tar.gz (183.5 kB view hashes)

Uploaded Source

Built Distribution

singlem-0.18.3-py3-none-any.whl (219.6 kB view hashes)

Uploaded Python 3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page