MersV1, Main, Exploration, bibRecord, 002233

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

Identifieur interne : 002233 ( Main/Exploration ); précédent : 002232; suivant : 002234

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

Auteurs : Yi Wang ; Henry C. M. Leung ; S. M. Yiu ; Francis Y. L. Chin

Source :

Bioinformatics [ 1367-4803 ] ; 2012.

RBID : PMC:3436824

Descripteurs français

KwdFr :
- Algorithmes, Analyse de séquence d'ADN (), Logiciel, Métagénomique (), Sensibilité et spécificité.
MESH :
- Algorithmes, Analyse de séquence d'ADN, Logiciel, Métagénomique, Sensibilité et spécificité.

English descriptors

KwdEn :
- Algorithms, Metagenomics (methods), Sensitivity and Specificity, Sequence Analysis, DNA (methods), Software.
MESH :
- methods : Metagenomics, Sequence Analysis, DNA.
- Algorithms, Sensitivity and Specificity, Software.

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 6× to 10×) 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

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436824

DOI: 10.1093/bioinformatics/bts397
PubMed: 22962452
PubMed Central: 3436824

Affiliations:

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<front><div type="abstract" xml:lang="en"><p><bold>Motivation:</bold>
 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.</p>
<p><bold>Results:</bold>
 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 <italic>w</italic>
 values are used to group reads with overlapping <italic>w</italic>
-mers, whereas reads from high-abundance species are grouped with high confidence based on a large <italic>w</italic>
 and then binning expands to low-abundance species using a relaxed (shorter) <italic>w</italic>
. Compared to the recent tools, TOSS and MetaCluster 4.0, MetaCluster 5.0 can find more species (especially those with low abundance of say 6× to 10×) and can achieve better sensitivity and specificity using less memory and running time.</p>
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<ext-link ext-link-type="uri" xlink:href="http://i.cs.hku.hk/~alse/MetaCluster/">http://i.cs.hku.hk/~alse/MetaCluster/</ext-link>
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<p><bold>Contact:</bold>
<email>chin@cs.hku.hk</email>
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MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample

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

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki

	Serveur d'exploration MERS
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