MetaCon: unsupervised clustering of metagenomic contigs with probabilistic k-mers statistics and coverage
Identifieur interne : 000484 ( Main/Exploration ); précédent : 000483; suivant : 000485MetaCon: unsupervised clustering of metagenomic contigs with probabilistic k-mers statistics and coverage
Auteurs : Jia Qian ; Matteo CominSource :
- BMC Bioinformatics [ 1471-2105 ] ; 2019.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
Abstract
Sequencing technologies allow the sequencing of microbial communities directly from the environment without prior culturing. Because assembly typically produces only genome fragments, also known as contigs, it is crucial to group them into putative species for further taxonomic profiling and down-streaming functional analysis. Taxonomic analysis of microbial communities requires contig clustering, a process referred to as binning, that is still one of the most challenging tasks when analyzing metagenomic data. The major problems are the lack of taxonomically related genomes in existing reference databases, the uneven abundance ratio of species, sequencing errors, and the limitations due to binning contig of different lengths.
In this context we present MetaCon a novel tool for unsupervised metagenomic contig binning based on probabilistic k-mers statistics and coverage. MetaCon uses a signature based on k-mers statistics that accounts for the different probability of appearance of a k-mer in different species, also contigs of different length are clustered in two separate phases. The effectiveness of MetaCon is demonstrated in both simulated and real datasets in comparison with state-of-art binning approaches such as CONCOCT, MaxBin and MetaBAT.
The online version of this article (10.1186/s12859-019-2904-4) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12859-019-2904-4
PubMed: 31757198
PubMed Central: 6873667
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000286
- to stream Pmc, to step Curation: 000286
- to stream Pmc, to step Checkpoint: 000248
- to stream PubMed, to step Corpus: 000357
- to stream PubMed, to step Curation: 000357
- to stream PubMed, to step Checkpoint: 000482
- to stream Ncbi, to step Merge: 002407
- to stream Ncbi, to step Curation: 002407
- to stream Ncbi, to step Checkpoint: 002407
- to stream Main, to step Merge: 000487
- to stream Main, to step Curation: 000484
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">MetaCon: unsupervised clustering of metagenomic contigs with probabilistic k-mers statistics and coverage</title><author><name sortKey="Qian, Jia" sort="Qian, Jia" uniqKey="Qian J" first="Jia" last="Qian">Jia Qian</name><affiliation><nlm:aff id="Aff1"></nlm:aff></affiliation></author><author><name sortKey="Comin, Matteo" sort="Comin, Matteo" uniqKey="Comin M" first="Matteo" last="Comin">Matteo Comin</name><affiliation><nlm:aff id="Aff1"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">31757198</idno><idno type="pmc">6873667</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6873667</idno><idno type="RBID">PMC:6873667</idno><idno type="doi">10.1186/s12859-019-2904-4</idno><date when="2019">2019</date><idno type="wicri:Area/Pmc/Corpus">000286</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000286</idno><idno type="wicri:Area/Pmc/Curation">000286</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000286</idno><idno type="wicri:Area/Pmc/Checkpoint">000248</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000248</idno><idno type="wicri:source">PubMed</idno><idno type="RBID">pubmed:31757198</idno><idno type="wicri:Area/PubMed/Corpus">000357</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000357</idno><idno type="wicri:Area/PubMed/Curation">000357</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000357</idno><idno type="wicri:Area/PubMed/Checkpoint">000482</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000482</idno><idno type="wicri:Area/Ncbi/Merge">002407</idno><idno type="wicri:Area/Ncbi/Curation">002407</idno><idno type="wicri:Area/Ncbi/Checkpoint">002407</idno><idno type="wicri:Area/Main/Merge">000487</idno><idno type="wicri:Area/Main/Curation">000484</idno><idno type="wicri:Area/Main/Exploration">000484</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">MetaCon: unsupervised clustering of metagenomic contigs with probabilistic k-mers statistics and coverage</title><author><name sortKey="Qian, Jia" sort="Qian, Jia" uniqKey="Qian J" first="Jia" last="Qian">Jia Qian</name><affiliation><nlm:aff id="Aff1"></nlm:aff></affiliation></author><author><name sortKey="Comin, Matteo" sort="Comin, Matteo" uniqKey="Comin M" first="Matteo" last="Comin">Matteo Comin</name><affiliation><nlm:aff id="Aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2019">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Cluster Analysis</term><term>Contig Mapping</term><term>Databases, Genetic</term><term>Metagenome</term><term>Metagenomics</term><term>Microbiota (genetics)</term><term>Probability</term><term>Statistics as Topic</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Analyse de regroupements</term><term>Bases de données génétiques</term><term>Cartographie de contigs</term><term>Microbiote (génétique)</term><term>Métagénome</term><term>Métagénomique</term><term>Probabilité</term><term>Statistiques comme sujet</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Microbiota</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Microbiote</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Cluster Analysis</term><term>Contig Mapping</term><term>Databases, Genetic</term><term>Metagenome</term><term>Metagenomics</term><term>Probability</term><term>Statistics as Topic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Analyse de regroupements</term><term>Bases de données génétiques</term><term>Cartographie de contigs</term><term>Métagénome</term><term>Métagénomique</term><term>Probabilité</term><term>Statistiques comme sujet</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Motivation</title><p>Sequencing technologies allow the sequencing of microbial communities directly from the environment without prior culturing. Because assembly typically produces only genome fragments, also known as contigs, it is crucial to group them into putative species for further taxonomic profiling and down-streaming functional analysis. Taxonomic analysis of microbial communities requires contig clustering, a process referred to as binning, that is still one of the most challenging tasks when analyzing metagenomic data. The major problems are the lack of taxonomically related genomes in existing reference databases, the uneven abundance ratio of species, sequencing errors, and the limitations due to binning contig of different lengths.</p></sec><sec><title>Results</title><p>In this context we present MetaCon a novel tool for unsupervised metagenomic contig binning based on probabilistic k-mers statistics and coverage. MetaCon uses a signature based on k-mers statistics that accounts for the different probability of appearance of a k-mer in different species, also contigs of different length are clustered in two separate phases. The effectiveness of MetaCon is demonstrated in both simulated and real datasets in comparison with state-of-art binning approaches such as CONCOCT, MaxBin and MetaBAT.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (10.1186/s12859-019-2904-4) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Staley, Jt" uniqKey="Staley J">JT Staley</name></author><author><name sortKey="Konopka, A" uniqKey="Konopka A">A Konopka</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Handelsman, J" uniqKey="Handelsman J">J Handelsman</name></author><author><name sortKey="Rondon, Mr" uniqKey="Rondon M">MR Rondon</name></author><author><name sortKey="Brady, Sf" uniqKey="Brady S">SF Brady</name></author><author><name sortKey="Clardy, J" uniqKey="Clardy J">J Clardy</name></author><author><name sortKey="Goodman, Rm" uniqKey="Goodman R">RM Goodman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Felczykowska, A" uniqKey="Felczykowska A">A Felczykowska</name></author><author><name sortKey="Bloch, Sk" uniqKey="Bloch S">SK Bloch</name></author><author><name sortKey="Nejman Fale Czyk, B" uniqKey="Nejman Fale Czyk B">B Nejman-Faleńczyk</name></author><author><name sortKey="Bara Ska, S" uniqKey="Bara Ska S">S Barańska</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mande, Ss" uniqKey="Mande S">SS Mande</name></author><author><name sortKey="Mohammed, Mh" uniqKey="Mohammed M">MH Mohammed</name></author><author><name sortKey="Ghosh, Ts" uniqKey="Ghosh T">TS Ghosh</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Alneberg, J" uniqKey="Alneberg J">J Alneberg</name></author><author><name sortKey="Brynjar Smari, B" uniqKey="Brynjar Smari B">B Brynjar Smári</name></author><author><name sortKey="Ino, Db" uniqKey="Ino D">DB Ino</name></author><author><name sortKey="Melanie, S" uniqKey="Melanie S">S Melanie</name></author><author><name sortKey="Joshua, Q" uniqKey="Joshua Q">Q Joshua</name></author><author><name sortKey="Umer Z, I" uniqKey="Umer Z I">I Umer Z</name></author><author><name sortKey="Leo, L" uniqKey="Leo L">L Leo</name></author><author><name sortKey="Nicholas J, L" uniqKey="Nicholas J L">L Nicholas J</name></author><author><name sortKey="Anders F, A" uniqKey="Anders F A">A Anders F</name></author><author><name sortKey="Christopher, Q" uniqKey="Christopher Q">Q Christopher</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bowers, Rm" uniqKey="Bowers R">RM Bowers</name></author><author><name sortKey="Clum, A" uniqKey="Clum A">A Clum</name></author><author><name sortKey="Tice, H" uniqKey="Tice H">H Tice</name></author><author><name sortKey="Lim, J" uniqKey="Lim J">J Lim</name></author><author><name sortKey="Singh, K" uniqKey="Singh K">K Singh</name></author><author><name sortKey="Ciobanu, D" uniqKey="Ciobanu D">D Ciobanu</name></author><author><name sortKey="Ngan, Cy" uniqKey="Ngan C">CY Ngan</name></author><author><name sortKey="Cheng, J F" uniqKey="Cheng J">J-F Cheng</name></author><author><name sortKey="Tringe, Sg" uniqKey="Tringe S">SG Tringe</name></author><author><name sortKey="Woyke, T" uniqKey="Woyke T">T Woyke</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sczyrba, A" uniqKey="Sczyrba A">A Sczyrba</name></author><author><name sortKey="Hofmann, P" uniqKey="Hofmann P">P Hofmann</name></author><author><name sortKey="Mchardy, Ac" uniqKey="Mchardy A">AC McHardy</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Huson, D H" uniqKey="Huson D">D. H. Huson</name></author><author><name sortKey="Auch, A F" uniqKey="Auch A">A. F. Auch</name></author><author><name sortKey="Qi, J" uniqKey="Qi J">J. Qi</name></author><author><name sortKey="Schuster, S C" uniqKey="Schuster S">S. C. Schuster</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wood, Derrick E" uniqKey="Wood D">Derrick E Wood</name></author><author><name sortKey="Salzberg, Steven L" uniqKey="Salzberg S">Steven L Salzberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ounit, R" uniqKey="Ounit R">R Ounit</name></author><author><name sortKey="Wanamaker, S" uniqKey="Wanamaker S">S Wanamaker</name></author><author><name sortKey="Close, Tj" uniqKey="Close T">TJ Close</name></author><author><name sortKey="Lonardi, S" uniqKey="Lonardi S">S Lonardi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Qian, J" uniqKey="Qian J">J Qian</name></author><author><name sortKey="Marchiori, D" uniqKey="Marchiori D">D Marchiori</name></author><author><name sortKey="Comin, M" uniqKey="Comin M">M Comin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Segata, Nicola" uniqKey="Segata N">Nicola Segata</name></author><author><name sortKey="Waldron, Levi" uniqKey="Waldron L">Levi Waldron</name></author><author><name sortKey="Ballarini, Annalisa" uniqKey="Ballarini A">Annalisa Ballarini</name></author><author><name sortKey="Narasimhan, Vagheesh" uniqKey="Narasimhan V">Vagheesh Narasimhan</name></author><author><name sortKey="Jousson, Olivier" uniqKey="Jousson O">Olivier Jousson</name></author><author><name sortKey="Huttenhower, Curtis" uniqKey="Huttenhower C">Curtis Huttenhower</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Eisen, Ja" uniqKey="Eisen J">JA Eisen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lindgreen, S" uniqKey="Lindgreen S">S Lindgreen</name></author><author><name sortKey="Adair, Kl" uniqKey="Adair K">KL Adair</name></author><author><name sortKey="Gardner, P" uniqKey="Gardner P">P Gardner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Girotto, S" uniqKey="Girotto S">S Girotto</name></author><author><name sortKey="Comin, M" uniqKey="Comin M">M Comin</name></author><author><name sortKey="Pizzi, C" uniqKey="Pizzi C">C Pizzi</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Leung, Hcm" uniqKey="Leung H">HCM Leung</name></author><author><name sortKey="Yiu, Sm" uniqKey="Yiu S">SM Yiu</name></author><author><name sortKey="Yang, B" uniqKey="Yang B">B Yang</name></author><author><name sortKey="Peng, Y" uniqKey="Peng Y">Y Peng</name></author><author><name sortKey="Wang, Y" uniqKey="Wang Y">Y Wang</name></author><author><name sortKey="Liu, Z" uniqKey="Liu Z">Z Liu</name></author><author><name sortKey="Chen, J" uniqKey="Chen J">J Chen</name></author><author><name sortKey="Qin, J" uniqKey="Qin J">J Qin</name></author><author><name sortKey="Li, R" uniqKey="Li R">R Li</name></author><author><name sortKey="Chin, Fyl" uniqKey="Chin F">FYL Chin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wu, Y W" uniqKey="Wu Y">Y-W Wu</name></author><author><name sortKey="Simmons, Ba" uniqKey="Simmons B">BA Simmons</name></author><author><name sortKey="Singer, Sw" uniqKey="Singer S">SW Singer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Imelfort, Michael" uniqKey="Imelfort M">Michael Imelfort</name></author><author><name sortKey="Parks, Donovan" uniqKey="Parks D">Donovan Parks</name></author><author><name sortKey="Woodcroft, Ben J" uniqKey="Woodcroft B">Ben J. Woodcroft</name></author><author><name sortKey="Dennis, Paul" uniqKey="Dennis P">Paul Dennis</name></author><author><name sortKey="Hugenholtz, Philip" uniqKey="Hugenholtz P">Philip Hugenholtz</name></author><author><name sortKey="Tyson, Gene W" uniqKey="Tyson G">Gene W. Tyson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kang, Dd" uniqKey="Kang D">DD Kang</name></author><author><name sortKey="Froula, J" uniqKey="Froula J">J Froula</name></author><author><name sortKey="Egan, R" uniqKey="Egan R">R Egan</name></author><author><name sortKey="Wang, Z" uniqKey="Wang Z">Z Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kantorovitz, Miriam R" uniqKey="Kantorovitz M">Miriam R. Kantorovitz</name></author><author><name sortKey="Robinson, Gene E" uniqKey="Robinson G">Gene E. Robinson</name></author><author><name sortKey="Sinha, Saurabh" uniqKey="Sinha S">Saurabh Sinha</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sims, Gregory E" uniqKey="Sims G">Gregory E. Sims</name></author><author><name sortKey="Jun, Se Ran" uniqKey="Jun S">Se-Ran Jun</name></author><author><name sortKey="Wu, Guohong A" uniqKey="Wu G">Guohong A. Wu</name></author><author><name sortKey="Kim, Sung Hou" uniqKey="Kim S">Sung-Hou Kim</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Comin, M" uniqKey="Comin M">M Comin</name></author><author><name sortKey="Antonello, M" uniqKey="Antonello M">M Antonello</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Comin, M" uniqKey="Comin M">M Comin</name></author><author><name sortKey="Verzotto, D" uniqKey="Verzotto D">D Verzotto</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Comin, M" uniqKey="Comin M">M Comin</name></author><author><name sortKey="Leoni, A" uniqKey="Leoni A">A Leoni</name></author><author><name sortKey="Schimd, M" uniqKey="Schimd M">M Schimd</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Comin, M" uniqKey="Comin M">M Comin</name></author><author><name sortKey="Antonello, M" uniqKey="Antonello M">M Antonello</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lippert, Ra" uniqKey="Lippert R">RA Lippert</name></author><author><name sortKey="Huang, H" uniqKey="Huang H">H Huang</name></author><author><name sortKey="Waterman, Ms" uniqKey="Waterman M">MS Waterman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="G, R" uniqKey="G R">R G</name></author><author><name sortKey="D, C" uniqKey="D C">C D</name></author><author><name sortKey="F, S" uniqKey="F S">S F</name></author><author><name sortKey="Ms, W" uniqKey="Ms W">W MS</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Regnier, M" uniqKey="Regnier M">M Régnier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Song, K" uniqKey="Song K">K Song</name></author><author><name sortKey="Ren, J" uniqKey="Ren J">J Ren</name></author><author><name sortKey="Reinert, G" uniqKey="Reinert G">G Reinert</name></author><author><name sortKey="Deng, M" uniqKey="Deng M">M Deng</name></author><author><name sortKey="Waterman, Ms" uniqKey="Waterman M">MS Waterman</name></author><author><name sortKey="Sun, F" uniqKey="Sun F">F Sun</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kaufmann, L" uniqKey="Kaufmann L">L Kaufmann</name></author><author><name sortKey="Rousseeuw, P" uniqKey="Rousseeuw P">P Rousseeuw</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Consortium, Hmp" uniqKey="Consortium H">HMP Consortium</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Boisvert, S" uniqKey="Boisvert S">S Boisvert</name></author><author><name sortKey="Raymond, F" uniqKey="Raymond F">F Raymond</name></author><author><name sortKey="Godzaridis, E" uniqKey="Godzaridis E">É Godzaridis</name></author><author><name sortKey="Laviolette, F" uniqKey="Laviolette F">F Laviolette</name></author><author><name sortKey="Corbeil, J" uniqKey="Corbeil J">J Corbeil</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sharon, I" uniqKey="Sharon I">I Sharon</name></author><author><name sortKey="Morowitz, Mj" uniqKey="Morowitz M">MJ Morowitz</name></author><author><name sortKey="Thomas, Bc" uniqKey="Thomas B">BC Thomas</name></author><author><name sortKey="Costello, Ek" uniqKey="Costello E">EK Costello</name></author><author><name sortKey="Relman, Da" uniqKey="Relman D">DA Relman</name></author><author><name sortKey="Banfield, Jf" uniqKey="Banfield J">JF Banfield</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Vinh, Lv" uniqKey="Vinh L">LV Vinh</name></author><author><name sortKey="Lang, Tv" uniqKey="Lang T">TV Lang</name></author><author><name sortKey="Binh, Lt" uniqKey="Binh L">LT Binh</name></author><author><name sortKey="Hoai, Tv" uniqKey="Hoai T">TV Hoai</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list></list><tree><noCountry><name sortKey="Comin, Matteo" sort="Comin, Matteo" uniqKey="Comin M" first="Matteo" last="Comin">Matteo Comin</name><name sortKey="Qian, Jia" sort="Qian, Jia" uniqKey="Qian J" first="Jia" last="Qian">Jia Qian</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000484 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000484 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= PMC:6873667
|texte= MetaCon: unsupervised clustering of metagenomic contigs with probabilistic k-mers statistics and coverage
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:31757198" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |