A two-phase binning algorithm using l-mer frequency on groups of non-overlapping reads

BACKGROUND: Metagenomics is the study of genetic materials derived directly from complex microbial samples, instead of from culture. One of the crucial steps in metagenomic analysis, referred to as “binning”, is to separate reads into clusters that represent genomes from closely related organisms. Among the existing binning methods, unsupervised methods base the classification on features extracted from reads, and especially taking advantage in case of the limitation of reference database availability. However, their performance, under various aspects, is still being investigated by recent theoretical and empirical studies. The one addressed in this paper is among those efforts to enhance the accuracy of the classification. RESULTS: This paper presents an unsupervised algorithm, called BiMeta, for binning of reads from different species in a metagenomic dataset. The algorithm consists of two phases. In the first phase of the algorithm, reads are grouped into groups based on overlap information between the reads. The second phase merges the groups by using an observation on l-mer frequency distribution of sets of non-overlapping reads. The experimental results on simulated and real datasets showed that BiMeta outperforms three state-of-the-art binning algorithms for both short and long reads (≥700 bp) datasets. CONCLUSIONS: This paper developed a novel and efficient algorithm for binning of metagenomic reads, which does not require any reference database. The software implementing the algorithm and all test datasets mentioned in this paper can be downloaded at http://it.hcmute.edu.vn/bioinfo/bimeta/index.htm. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13015-014-0030-4) contains supplementary material, which is available to authorized users.