Article: Meta-IDBA: A de Novo assembler for metagenomic data

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TitleMeta-IDBA: A de Novo assembler for metagenomic data
AuthorsPeng, Y1
Leung, HCM1
Yiu, SM1
Chin, FYL1
Issue Date2011
PublisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/
CitationThe 19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology (ISMB/ECCB 2011), Vienna, Austria, 17-19 july 2011. In Bioinformatics, 2011, v. 27 n. 13, p. i94-i101, article no. btr216 [How to Cite?]
DOI: http://dx.doi.org/10.1093/bioinformatics/btr216
AbstractMotivation: 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. © The Author(s) 2011. Published by Oxford University Press.
DescriptionThis Open Access Journal issue is the ISMB/ECCB 2011 Proceedings
ISSN1367-4803
2011 Impact Factor: 5.468
2011 SCImago Journal Rankings: 1.118
DOIhttp://dx.doi.org/10.1093/bioinformatics/btr216
ISI Accession Number IDWOS:000291752600012
PubMed Central IDPMC3117360
ReferencesReferences in Scopus
DC Field
Value
dc.contributor.authorPeng, Y
dc.contributor.authorLeung, HCM
dc.contributor.authorYiu, SM
dc.contributor.authorChin, FYL
dc.date.accessioned2011-09-23T06:04:37Z
dc.date.available2011-09-23T06:04:37Z
dc.date.issued2011
dc.description.abstractMotivation: 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. © The Author(s) 2011. Published by Oxford University Press.
dc.description.naturelink_to_OA_fulltext
dc.descriptionThis Open Access Journal issue is the ISMB/ECCB 2011 Proceedings
dc.description.otherThe 19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology (ISMB/ECCB 2011), Vienna, Austria, 17-19 july 2011. In Bioinformatics, 2011, v. 27 n. 13, p. i94-i101, article no. btr216
dc.identifier.citationThe 19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology (ISMB/ECCB 2011), Vienna, Austria, 17-19 july 2011. In Bioinformatics, 2011, v. 27 n. 13, p. i94-i101, article no. btr216 [How to Cite?]
DOI: http://dx.doi.org/10.1093/bioinformatics/btr216
dc.identifier.citeulike9424946
dc.identifier.doihttp://dx.doi.org/10.1093/bioinformatics/btr216
dc.identifier.epagei101
dc.identifier.hkuros196172
dc.identifier.hkuros187808
dc.identifier.isiWOS:000291752600012
dc.identifier.issn1367-4803
2011 Impact Factor: 5.468
2011 SCImago Journal Rankings: 1.118
dc.identifier.issue13
dc.identifier.pmcidPMC3117360
dc.identifier.pmid21685107
dc.identifier.scopuseid_2-s2.0-79959422558
dc.identifier.spagei94
dc.identifier.urihttp://hdl.handle.net/10722/140006
dc.identifier.volume27
dc.languageeng
dc.publisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/
dc.publisher.placeUnited Kingdom
dc.relation.ispartofBioinformatics
dc.relation.referencesReferences in Scopus
dc.subject.meshAlgorithms
dc.subject.meshEscherichia coli - classification - genetics - isolation and purification
dc.subject.meshGenome, Bacterial
dc.subject.meshMetagenomics - methods
dc.subject.meshSoftware
dc.titleMeta-IDBA: A de Novo assembler for metagenomic data
dc.typeArticle
Author Affiliations
  1. The University of Hong Kong