Benchmarking Metagenomics Tools for Taxonomic Classification

Cell. 2019 Aug 8;178(4):779-794. doi: 10.1016/j.cell.2019.07.010.


Metagenomic sequencing is revolutionizing the detection and characterization of microbial species, and a wide variety of software tools are available to perform taxonomic classification of these data. The fast pace of development of these tools and the complexity of metagenomic data make it important that researchers are able to benchmark their performance. Here, we review current approaches for metagenomic analysis and evaluate the performance of 20 metagenomic classifiers using simulated and experimental datasets. We describe the key metrics used to assess performance, offer a framework for the comparison of additional classifiers, and discuss the future of metagenomic data analysis.

Publication types

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

MeSH terms

  • Bacteria / classification*
  • Bacteria / genetics
  • Benchmarking / methods*
  • Databases, Genetic
  • Fungi / classification*
  • Fungi / genetics
  • Metagenome / genetics*
  • Metagenomics / methods*
  • Phylogeny
  • Polymerase Chain Reaction
  • Sequence Analysis, DNA
  • Software
  • Viruses / classification*
  • Viruses / genetics