CoMeta: classification of metagenomes using k-mers

PLoS One. 2015 Apr 17;10(4):e0121453. doi: 10.1371/journal.pone.0121453. eCollection 2015.

Abstract

Nowadays, the study of environmental samples has been developing rapidly. Characterization of the environment composition broadens the knowledge about the relationship between species composition and environmental conditions. An important element of extracting the knowledge of the sample composition is to compare the extracted fragments of DNA with sequences derived from known organisms. In the presented paper, we introduce an algorithm called CoMeta (Classification of metagenomes), which assigns a query read (a DNA fragment) into one of the groups previously prepared by the user. Typically, this is one of the taxonomic rank (e.g., phylum, genus), however prepared groups may contain sequences having various functions. In CoMeta, we used the exact method for read classification using short subsequences (k-mers) and fast program for indexing large set of k-mers. In contrast to the most popular methods based on BLAST, where the query is compared with each reference sequence, we begin the classification from the top of the taxonomy tree to reduce the number of comparisons. The presented experimental study confirms that CoMeta outperforms other programs used in this context. CoMeta is available at https://github.com/jkawulok/cometa under a free GNU GPL 2 license.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Databases, Genetic
  • Internet
  • Metagenomics / methods*
  • Sequence Analysis, DNA
  • User-Computer Interface*

Grant support

This work was supported by the Polish National Science Centre under the project DEC-2012/05/B/ST6/03148 and the European Union from the European Social Fund (grant agreement number: UDA-POKL.04.01.01-00-106/09). The work was performed using the infrastructure supported by POIG.02.03.01-24-099/13 grant: "GeCONiI---Upper Silesian Center for Computational Science and Engineering". This research was supported in part by PL-Grid Infrastructure. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.