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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
2012 Impact Factor: 5.323
2012 SCImago Journal Rankings: 4.223
 
DOIhttp://dx.doi.org/10.1093/bioinformatics/btr216
 
PubMed Central IDPMC3117360
 
ISI Accession Number IDWOS:000291752600012
 
ReferencesReferences in Scopus
 
DC FieldValue
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.eissn1460-2059
 
dc.identifier.epagei101
 
dc.identifier.hkuros196172
 
dc.identifier.hkuros187808
 
dc.identifier.isiWOS:000291752600012
 
dc.identifier.issn1367-4803
2012 Impact Factor: 5.323
2012 SCImago Journal Rankings: 4.223
 
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
 
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Author Affiliations
  1. The University of Hong Kong