MetaCluster 5.0: A Two-Round Binning Approach for Metagenomic Data for Low-Abundance Species in a Noisy Sample

Bioinformatics. 2012 Sep 15;28(18):i356-i362. doi: 10.1093/bioinformatics/bts397.

Abstract

Motivation: Metagenomic binning remains an important topic in metagenomic analysis. Existing unsupervised binning methods for next-generation sequencing (NGS) reads do not perform well on (i) samples with low-abundance species or (ii) samples (even with high abundance) when there are many extremely low-abundance species. These two problems are common for real metagenomic datasets. Binning methods that can solve these problems are desirable.

Results: We proposed a two-round binning method (MetaCluster 5.0) that aims at identifying both low-abundance and high-abundance species in the presence of a large amount of noise due to many extremely low-abundance species. In summary, MetaCluster 5.0 uses a filtering strategy to remove noise from the extremely low-abundance species. It separate reads of high-abundance species from those of low-abundance species in two different rounds. To overcome the issue of low coverage for low-abundance species, multiple w values are used to group reads with overlapping w-mers, whereas reads from high-abundance species are grouped with high confidence based on a large w and then binning expands to low-abundance species using a relaxed (shorter) w. Compared to the recent tools, TOSS and MetaCluster 4.0, MetaCluster 5.0 can find more species (especially those with low abundance of say 6× to 10×) and can achieve better sensitivity and specificity using less memory and running time.

Availability: http://i.cs.hku.hk/~alse/MetaCluster/

Contact: chin@cs.hku.hk.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Metagenomics / methods*
  • Sensitivity and Specificity
  • Sequence Analysis, DNA / methods
  • Software*