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Meta-IDBA: a de Novo assembler for metagenomic data

Meta-IDBA: a de Novo assembler for metagenomic data Motivation: Next-generation sequencing techniques allow us to generate reads from a microbial environment in order to analyze the microbial community. However, assembling of a set of mixed reads from different species to form contigs is a bottleneck of metagenomic research. Although there are many assemblers for assembling reads from a single genome, there are no assemblers for assembling reads in metagenomic data without reference genome sequences. Moreover, the performances of these assemblers on metagenomic data are far from satisfactory, because of the existence of common regions in the genomes of subspecies and species, which make the assembly problem much more complicated.Results: We introduce the Meta-IDBA algorithm for assembling reads in metagenomic data, which contain multiple genomes from different species. There are two core steps in Meta-IDBA. It first tries to partition the de Bruijn graph into isolated components of different species based on an important observation. Then, for each component, it captures the slight variants of the genomes of subspecies from the same species by multiple alignments and represents the genome of one species, using a consensus sequence. Comparison of the performances of Meta-IDBA and existing assemblers, such as Velvet and Abyss for different metagenomic datasets shows that Meta-IDBA can reconstruct longer contigs with similar accuracy.Availability: Meta-IDBA toolkit is available at our website http://www.cs.hku.hk/~alse/metaidba.Contact: chin@cs.hku.hk http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Bioinformatics Oxford University Press

Meta-IDBA: a de Novo assembler for metagenomic data

Peng, Yu; Leung, Henry C. M.; Yiu, S. M.; Chin, Francis Y. L.
Bioinformatics , Volume 27 (13): 8 – Jun 14, 2011
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References (24)

Publisher
Oxford University Press
Copyright
© The Author(s) 2011. Published by Oxford University Press.
ISSN
1367-4803
eISSN
1460-2059
DOI
10.1093/bioinformatics/btr216
pmid
21685107
Publisher site
See Article on Publisher Site

Abstract

Motivation: Next-generation sequencing techniques allow us to generate reads from a microbial environment in order to analyze the microbial community. However, assembling of a set of mixed reads from different species to form contigs is a bottleneck of metagenomic research. Although there are many assemblers for assembling reads from a single genome, there are no assemblers for assembling reads in metagenomic data without reference genome sequences. Moreover, the performances of these assemblers on metagenomic data are far from satisfactory, because of the existence of common regions in the genomes of subspecies and species, which make the assembly problem much more complicated.Results: We introduce the Meta-IDBA algorithm for assembling reads in metagenomic data, which contain multiple genomes from different species. There are two core steps in Meta-IDBA. It first tries to partition the de Bruijn graph into isolated components of different species based on an important observation. Then, for each component, it captures the slight variants of the genomes of subspecies from the same species by multiple alignments and represents the genome of one species, using a consensus sequence. Comparison of the performances of Meta-IDBA and existing assemblers, such as Velvet and Abyss for different metagenomic datasets shows that Meta-IDBA can reconstruct longer contigs with similar accuracy.Availability: Meta-IDBA toolkit is available at our website http://www.cs.hku.hk/~alse/metaidba.Contact: chin@cs.hku.hk

Journal

Bioinformatics – Oxford University Press

Published: Jun 14, 2011

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