MetaGen: reference-free learning with multiple metagenomic samples

Genome Biol. 2017 Oct 3;18(1):187. doi: 10.1186/s13059-017-1323-y.


A major goal of metagenomics is to identify and study the entire collection of microbial species in a set of targeted samples. We describe a statistical metagenomic algorithm that simultaneously identifies microbial species and estimates their abundances without using reference genomes. As a trade-off, we require multiple metagenomic samples, usually ≥10 samples, to get highly accurate binning results. Compared to reference-free methods based primarily on k-mer distributions or coverage information, the proposed approach achieves a higher species binning accuracy and is particularly powerful when sequencing coverage is low. We demonstrated the performance of this new method through both simulation and real metagenomic studies. The MetaGen software is available at .

Keywords: Binning; Metagenomics; Mixture model; Multinomial; Unsupervised learning.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, N.I.H., Extramural

MeSH terms

  • Bayes Theorem
  • Diabetes Mellitus, Type 2 / microbiology
  • Humans
  • Inflammatory Bowel Diseases / microbiology
  • Metagenomics / methods*
  • Obesity / microbiology
  • Software