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Conference Paper: MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample

TitleMetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample
Authors
Issue Date2012
PublisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/
Citation
The 11th European Conference on Computational Biology (ECCB'12), Basel, Switzerland, 9-12 September 2012. In Bioinformatics, 2012, v. 28 n. 18, p. i356-i362 How to Cite?
AbstractMOTIVATION: Metagenomic binning remains an important topic in metagenomic analysis. Existing unsupervised binning methods for next-generation sequencing (NGS) reads do not perform well on (i) samples with low-abundance species or (ii) samples (even with high abundance) when there are many extremely low-abundance species. These two problems are common for real metagenomic datasets. Binning methods that can solve these problems are desirable. RESULTS: We proposed a two-round binning method (MetaCluster 5.0) that aims at identifying both low-abundance and high-abundance species in the presence of a large amount of noise due to many extremely low-abundance species. In summary, MetaCluster 5.0 uses a filtering strategy to remove noise from the extremely low-abundance species. It separate reads of high-abundance species from those of low-abundance species in two different rounds. To overcome the issue of low coverage for low-abundance species, multiple w values are used to group reads with overlapping w-mers, whereas reads from high-abundance species are grouped with high confidence based on a large w and then binning expands to low-abundance species using a relaxed (shorter) w. Compared to the recent tools, TOSS and MetaCluster 4.0, MetaCluster 5.0 can find more species (especially those with low abundance of say 6x to 10x) and can achieve better sensitivity and specificity using less memory and running time. AVAILABILITY: http://i.cs.hku.hk/alse/MetaCluster/ CONTACT: chin@cs.hku.hk.
DescriptionAll proceedings papers are available as open access at: OUP Bioinformatics (http://www.eccb12.org/proceedings-talks)
Persistent Identifierhttp://hdl.handle.net/10722/165872
ISSN
2015 Impact Factor: 5.766
2015 SCImago Journal Rankings: 4.643
PubMed Central ID
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorWang, Yen_US
dc.contributor.authorLeung, HCMen_US
dc.contributor.authorYiu, SMen_US
dc.contributor.authorChin, FYLen_US
dc.date.accessioned2012-09-20T08:24:40Z-
dc.date.available2012-09-20T08:24:40Z-
dc.date.issued2012en_US
dc.identifier.citationThe 11th European Conference on Computational Biology (ECCB'12), Basel, Switzerland, 9-12 September 2012. In Bioinformatics, 2012, v. 28 n. 18, p. i356-i362en_US
dc.identifier.issn1367-4803-
dc.identifier.urihttp://hdl.handle.net/10722/165872-
dc.descriptionAll proceedings papers are available as open access at: OUP Bioinformatics (http://www.eccb12.org/proceedings-talks)-
dc.description.abstractMOTIVATION: Metagenomic binning remains an important topic in metagenomic analysis. Existing unsupervised binning methods for next-generation sequencing (NGS) reads do not perform well on (i) samples with low-abundance species or (ii) samples (even with high abundance) when there are many extremely low-abundance species. These two problems are common for real metagenomic datasets. Binning methods that can solve these problems are desirable. RESULTS: We proposed a two-round binning method (MetaCluster 5.0) that aims at identifying both low-abundance and high-abundance species in the presence of a large amount of noise due to many extremely low-abundance species. In summary, MetaCluster 5.0 uses a filtering strategy to remove noise from the extremely low-abundance species. It separate reads of high-abundance species from those of low-abundance species in two different rounds. To overcome the issue of low coverage for low-abundance species, multiple w values are used to group reads with overlapping w-mers, whereas reads from high-abundance species are grouped with high confidence based on a large w and then binning expands to low-abundance species using a relaxed (shorter) w. Compared to the recent tools, TOSS and MetaCluster 4.0, MetaCluster 5.0 can find more species (especially those with low abundance of say 6x to 10x) and can achieve better sensitivity and specificity using less memory and running time. AVAILABILITY: http://i.cs.hku.hk/alse/MetaCluster/ CONTACT: chin@cs.hku.hk.-
dc.languageengen_US
dc.publisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/en_US
dc.relation.ispartofBioinformaticsen_US
dc.rightsCreative Commons: Attribution 3.0 Hong Kong Licenseen_US
dc.titleMetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sampleen_US
dc.typeConference_Paperen_US
dc.identifier.emailWang, Y: h1095106@hku.hken_US
dc.identifier.emailLeung, HCM: cmleung2@cs.hku.hken_US
dc.identifier.emailYiu, SM: smyiu@cs.hku.hken_US
dc.identifier.emailChin, FYL: chin@cs.hku.hk-
dc.identifier.authorityLeung, HCM=rp00144en_US
dc.identifier.authorityYiu, SM=rp00207en_US
dc.identifier.authorityChin, FYL=rp00105en_US
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1093/bioinformatics/bts397-
dc.identifier.pmid22962452-
dc.identifier.pmcidPMC3436824-
dc.identifier.scopuseid_2-s2.0-84866458820-
dc.identifier.hkuros202743en_US
dc.identifier.hkuros211202-
dc.identifier.volume28en_US
dc.identifier.issue18en_US
dc.identifier.spagei356en_US
dc.identifier.epagei362en_US
dc.identifier.isiWOS:000308532300008-
dc.publisher.placeUnited Kingdom-
dc.description.otherThe 11th European Conference on Computational Biology (ECCB'12), Basel, Switzerland, 9-12 September 2012. In Bioinformatics, 2012, v. 28 n. 18, p. i356-i362-
dc.identifier.citeulike11201412-

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