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Conference Paper: Meta-IDBA: A de Novo assembler for metagenomic data

TitleMeta-IDBA: A de Novo assembler for metagenomic data
Authors
Issue Date2011
PublisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/
Citation
The 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?
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.
Persistent Identifierhttp://hdl.handle.net/10722/140006
ISSN
2015 Impact Factor: 5.766
2015 SCImago Journal Rankings: 4.643
PubMed Central ID
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorPeng, Yen_HK
dc.contributor.authorLeung, HCMen_HK
dc.contributor.authorYiu, SMen_HK
dc.contributor.authorChin, FYLen_HK
dc.date.accessioned2011-09-23T06:04:37Z-
dc.date.available2011-09-23T06:04:37Z-
dc.date.issued2011en_HK
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. btr216en_HK
dc.identifier.issn1367-4803en_HK
dc.identifier.urihttp://hdl.handle.net/10722/140006-
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.en_HK
dc.languageengen_US
dc.publisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/en_HK
dc.relation.ispartofBioinformaticsen_HK
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 dataen_HK
dc.typeConference_Paperen_HK
dc.identifier.emailLeung, HCM:cmleung2@cs.hku.hken_HK
dc.identifier.emailYiu, SM:smyiu@cs.hku.hken_HK
dc.identifier.emailChin, FYL:chin@cs.hku.hken_HK
dc.identifier.authorityLeung, HCM=rp00144en_HK
dc.identifier.authorityYiu, SM=rp00207en_HK
dc.identifier.authorityChin, FYL=rp00105en_HK
dc.description.naturelink_to_OA_fulltext-
dc.identifier.doi10.1093/bioinformatics/btr216en_HK
dc.identifier.pmid21685107-
dc.identifier.pmcidPMC3117360-
dc.identifier.scopuseid_2-s2.0-79959422558en_HK
dc.identifier.hkuros196172en_US
dc.identifier.hkuros187808-
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-79959422558&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume27en_HK
dc.identifier.issue13en_HK
dc.identifier.spagei94en_HK
dc.identifier.epagei101en_HK
dc.identifier.eissn1460-2059-
dc.identifier.isiWOS:000291752600012-
dc.publisher.placeUnited Kingdomen_HK
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.scopusauthoridPeng, Y=54393903900en_HK
dc.identifier.scopusauthoridLeung, HCM=35233742700en_HK
dc.identifier.scopusauthoridYiu, SM=7003282240en_HK
dc.identifier.scopusauthoridChin, FYL=7005101915en_HK
dc.identifier.citeulike9424946-

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