Introduction

Compared with traditional algorithms for long metagenomic sequence classification, characterizing microorganisms' taxonomic and functional abundance based on tens of millions of very short reads are much more challenging. We describe an efficient composition and phylogeny-based algorithm [Metagenome Composition Vector (MetaCV)] to classify very short metagenomic reads (75-100 bp) into specific taxonomic and functional groups. We applied MetaCV to the Meta-HIT data (371-Gb 75-bp reads of 109 human gut metagenomes), and this single-read-based, instead of assembly-based, classification has a high resolution to characterize the composition and structure of human gut microbiota, especially for low abundance species. Most strikingly, it only took MetaCV 10 days to do all the computation work on a server with five 24-core nodes. To our knowledge, MetaCV, benefited from the strategy of composition comparison, is the first algorithm that can classify millions of very short reads within affordable time.

Publications

  1. Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms.
    Cite this
    Liu J, Wang H, Yang H, Zhang Y, Wang J, Zhao F, Qi J, 2013-01-01 - Nucleic acids research

Credits

  1. Jiemeng Liu
    Developer

  2. Haifeng Wang
    Developer

  3. Hongxing Yang
    Developer

  4. Yizhe Zhang
    Developer

  5. Jinfeng Wang
    Developer

  6. Fangqing Zhao
    Developer

  7. Ji Qi
    Investigator

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Summary
AccessionBT001437
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Submitted ByJi Qi