title: A robust and accurate binning algorithm for metagenomic sequences with arbitrary species abundance ratio.
abstract: BACKGROUND
  With the rapid development of next-generation sequencing techniques, metagenomics, also known as environmental genomics, has emerged as an exciting research area that enables us to analyze the microbial environment in which we live. An important step for metagenomic data analysis is the identification and taxonomic characterization of DNA fragments (reads or contigs) resulting from sequencing a sample of mixed species. This step is referred to as 'binning'. Binning algorithms that are based on sequence similarity and sequence composition markers rely heavily on the reference genomes of known microorganisms or phylogenetic markers. Due to the limited availability of reference genomes and the bias and low availability of markers, these algorithms may not be applicable in all cases. Unsupervised binning algorithms which can handle fragments from unknown species provide an alternative approach. However, existing unsupervised binning algorithms only work on datasets either with balanced species abundance ratios or rather different abundance ratios, but not both.
  
  
  RESULTS
  In this article, we present MetaCluster 3.0, an integrated binning method based on the unsupervised top--down separation and bottom--up merging strategy, which can bin metagenomic fragments of species with very balanced abundance ratios (say 1:1) to very different abundance ratios (e.g. 1:24) with consistently higher accuracy than existing methods.
  
  
  BACKGROUND
  MetaCluster 3.0 can be downloaded at http://i.cs.hku.hk/~alse/MetaCluster/.
authors.affiliation: Department of Computer Science, The University of Hong Kong, Hong Kong. cmleung2@cs.hku.hk
authors.forename: Henry C M
authors.initials: HC
authors.lastname: Leung
authors.forename: S M
authors.initials: SM
authors.lastname: Yiu
authors.forename: Bin
authors.initials: B
authors.lastname: Yang
authors.forename: Yu
authors.initials: Y
authors.lastname: Peng
authors.forename: Yi
authors.initials: Y
authors.lastname: Wang
authors.forename: Zhihua
authors.initials: Z
authors.lastname: Liu
authors.forename: Jingchi
authors.initials: J
authors.lastname: Chen
authors.forename: Junjie
authors.initials: J
authors.lastname: Qin
authors.forename: Ruiqiang
authors.initials: R
authors.lastname: Li
authors.forename: Francis Y L
authors.initials: FY
authors.lastname: Chin
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D056186:Metagenomics / Q000379:methods*; D017422:Sequence Analysis, DNA