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- Publisher Website: 10.1093/bioinformatics/bts397
- Scopus: eid_2-s2.0-84866458820
- PMID: 22962452
- WOS: WOS:000308532300008
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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
Title | MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample |
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Authors | |
Issue Date | 2012 |
Publisher | Oxford 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? |
Abstract | MOTIVATION: 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. |
Description | All proceedings papers are available as open access at: OUP Bioinformatics (http://www.eccb12.org/proceedings-talks) |
Persistent Identifier | http://hdl.handle.net/10722/165872 |
ISSN | 2023 Impact Factor: 4.4 2023 SCImago Journal Rankings: 2.574 |
PubMed Central ID | |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Wang, Y | en_US |
dc.contributor.author | Leung, HCM | en_US |
dc.contributor.author | Yiu, SM | en_US |
dc.contributor.author | Chin, FYL | en_US |
dc.date.accessioned | 2012-09-20T08:24:40Z | - |
dc.date.available | 2012-09-20T08:24:40Z | - |
dc.date.issued | 2012 | en_US |
dc.identifier.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 | en_US |
dc.identifier.issn | 1367-4803 | - |
dc.identifier.uri | http://hdl.handle.net/10722/165872 | - |
dc.description | All proceedings papers are available as open access at: OUP Bioinformatics (http://www.eccb12.org/proceedings-talks) | - |
dc.description.abstract | MOTIVATION: 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.language | eng | en_US |
dc.publisher | Oxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/ | en_US |
dc.relation.ispartof | Bioinformatics | en_US |
dc.title | MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample | en_US |
dc.type | Conference_Paper | en_US |
dc.identifier.email | Wang, Y: h1095106@hku.hk | en_US |
dc.identifier.email | Leung, HCM: cmleung2@cs.hku.hk | en_US |
dc.identifier.email | Yiu, SM: smyiu@cs.hku.hk | en_US |
dc.identifier.email | Chin, FYL: chin@cs.hku.hk | - |
dc.identifier.authority | Leung, HCM=rp00144 | en_US |
dc.identifier.authority | Yiu, SM=rp00207 | en_US |
dc.identifier.authority | Chin, FYL=rp00105 | en_US |
dc.description.nature | published_or_final_version | - |
dc.identifier.doi | 10.1093/bioinformatics/bts397 | - |
dc.identifier.pmid | 22962452 | - |
dc.identifier.pmcid | PMC3436824 | - |
dc.identifier.scopus | eid_2-s2.0-84866458820 | - |
dc.identifier.hkuros | 202743 | en_US |
dc.identifier.hkuros | 211202 | - |
dc.identifier.volume | 28 | en_US |
dc.identifier.issue | 18 | en_US |
dc.identifier.spage | i356 | en_US |
dc.identifier.epage | i362 | en_US |
dc.identifier.isi | WOS:000308532300008 | - |
dc.publisher.place | United Kingdom | - |
dc.description.other | 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 | - |
dc.identifier.citeulike | 11201412 | - |
dc.identifier.issnl | 1367-4803 | - |