Assessing the performance of different approaches for functional and taxonomic annotation of metagenomes.
Identifieur interne : 000337 ( PubMed/Corpus ); précédent : 000336; suivant : 000338Assessing the performance of different approaches for functional and taxonomic annotation of metagenomes.
Auteurs : Javier Tamames ; Marta Cobo-Sim N ; Fernando Puente-SánchezSource :
- BMC genomics [ 1471-2164 ] ; 2019.
Abstract
Metagenomes can be analysed using different approaches and tools. One of the most important distinctions is the way to perform taxonomic and functional assignment, choosing between the use of assembly algorithms or the direct analysis of raw sequence reads instead by homology searching, k-mer analysys, or detection of marker genes. Many instances of each approach can be found in the literature, but to the best of our knowledge no evaluation of their different performances has been carried on, and we question if their results are comparable.
DOI: 10.1186/s12864-019-6289-6
PubMed: 31823721
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pubmed:31823721Le document en format XML
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<author><name sortKey="Tamames, Javier" sort="Tamames, Javier" uniqKey="Tamames J" first="Javier" last="Tamames">Javier Tamames</name>
<affiliation><nlm:affiliation>Systems Biology Department, Centro Nacional de Biotecnología, CSIC, C/Darwin 3, 28049, Madrid, Spain. jtamames@cnb.csic.es.</nlm:affiliation>
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<author><name sortKey="Cobo Sim N, Marta" sort="Cobo Sim N, Marta" uniqKey="Cobo Sim N M" first="Marta" last="Cobo-Sim N">Marta Cobo-Sim N</name>
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<author><name sortKey="Puente Sanchez, Fernando" sort="Puente Sanchez, Fernando" uniqKey="Puente Sanchez F" first="Fernando" last="Puente-Sánchez">Fernando Puente-Sánchez</name>
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<front><div type="abstract" xml:lang="en">Metagenomes can be analysed using different approaches and tools. One of the most important distinctions is the way to perform taxonomic and functional assignment, choosing between the use of assembly algorithms or the direct analysis of raw sequence reads instead by homology searching, k-mer analysys, or detection of marker genes. Many instances of each approach can be found in the literature, but to the best of our knowledge no evaluation of their different performances has been carried on, and we question if their results are comparable.</div>
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<ArticleTitle>Assessing the performance of different approaches for functional and taxonomic annotation of metagenomes.</ArticleTitle>
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<Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Metagenomes can be analysed using different approaches and tools. One of the most important distinctions is the way to perform taxonomic and functional assignment, choosing between the use of assembly algorithms or the direct analysis of raw sequence reads instead by homology searching, k-mer analysys, or detection of marker genes. Many instances of each approach can be found in the literature, but to the best of our knowledge no evaluation of their different performances has been carried on, and we question if their results are comparable.</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="RESULTS">We have analysed several real and mock metagenomes using different methodologies and tools, and compared the resulting taxonomic and functional profiles. Our results show that database completeness (the representation of diverse organisms and taxa in it) is the main factor determining the performance of the methods relying on direct read assignment either by homology, k-mer composition or similarity to marker genes, while methods relying on assembly and assignment of predicted genes are most influenced by metagenomic size, that in turn determines the completeness of the assembly (the percentage of read that were assembled).</AbstractText>
<AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">Although differences exist, taxonomic profiles are rather similar between raw read assignment and assembly assignment methods, while they are more divergent for methods based on k-mers and marker genes. Regarding functional annotation, analysis of raw reads retrieves more functions, but it also makes a substantial number of over-predictions. Assembly methods are more advantageous as the size of the metagenome grows bigger.</AbstractText>
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<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Tamames</LastName>
<ForeName>Javier</ForeName>
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<Identifier Source="ORCID">http://orcid.org/0000-0003-4547-8932</Identifier>
<AffiliationInfo><Affiliation>Systems Biology Department, Centro Nacional de Biotecnología, CSIC, C/Darwin 3, 28049, Madrid, Spain. jtamames@cnb.csic.es.</Affiliation>
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<Language>eng</Language>
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<Agency>Ministerio de Economía, Industria y Competitividad, Gobierno de España</Agency>
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<KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Assembly</Keyword>
<Keyword MajorTopicYN="N">Functional annotation</Keyword>
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<Keyword MajorTopicYN="N">Taxonomic annotation</Keyword>
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</ArticleIdList>
<ReferenceList><Reference><Citation>Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):594-9</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22184244</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Front Microbiol. 2016 Mar 31;7:433</Citation>
<ArticleIdList><ArticleId IdType="pubmed">27065987</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Appl Environ Microbiol. 2012 Jan;78(2):549-59</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22081564</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Front Microbiol. 2018 Oct 02;9:2353</Citation>
<ArticleIdList><ArticleId IdType="pubmed">30333812</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>PLoS One. 2014 Aug 22;9(8):e105776</Citation>
<ArticleIdList><ArticleId IdType="pubmed">25148512</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Nat Methods. 2017 Nov;14(11):1063-1071</Citation>
<ArticleIdList><ArticleId IdType="pubmed">28967888</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Bioinformatics. 2015 May 15;31(10):1674-6</Citation>
<ArticleIdList><ArticleId IdType="pubmed">25609793</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Nucleic Acids Res. 2014 Jan;42(Database issue):D581-91</Citation>
<ArticleIdList><ArticleId IdType="pubmed">24225323</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>ISME J. 2012 Apr;6(4):898-901</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22030673</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Genome Res. 2016 Dec;26(12):1721-1729</Citation>
<ArticleIdList><ArticleId IdType="pubmed">27852649</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Syst Appl Microbiol. 2013 Jun;36(4):215-7</Citation>
<ArticleIdList><ArticleId IdType="pubmed">23453737</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Genome Biol. 2014 Mar 03;15(3):R46</Citation>
<ArticleIdList><ArticleId IdType="pubmed">24580807</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Appl Environ Microbiol. 2008 Mar;74(5):1453-63</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18192407</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Genome Res. 2017 May;27(5):824-834</Citation>
<ArticleIdList><ArticleId IdType="pubmed">28298430</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Bioinformatics. 2014 Dec 15;30(24):3548-55</Citation>
<ArticleIdList><ArticleId IdType="pubmed">25359891</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Nat Methods. 2012 Mar 04;9(4):357-9</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22388286</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Nat Methods. 2015 Oct;12(10):902-3</Citation>
<ArticleIdList><ArticleId IdType="pubmed">26418763</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Nature. 2011 Nov 06;480(7377):368-71</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22056985</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Nucleic Acids Res. 2014 Apr;42(8):e73</Citation>
<ArticleIdList><ArticleId IdType="pubmed">24589583</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Nucleic Acids Res. 1999 Jan 1;27(1):29-34</Citation>
<ArticleIdList><ArticleId IdType="pubmed">9847135</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>R Soc Open Sci. 2015 Apr 22;2(4):140219</Citation>
<ArticleIdList><ArticleId IdType="pubmed">26064626</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Bioinformatics. 2008 Sep 15;24(18):2124-5</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18625611</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Nature. 2007 Oct 18;449(7164):804-10</Citation>
<ArticleIdList><ArticleId IdType="pubmed">17943116</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Nat Methods. 2015 Jan;12(1):59-60</Citation>
<ArticleIdList><ArticleId IdType="pubmed">25402007</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Genom Data. 2015 Mar 24;4:73-5</Citation>
<ArticleIdList><ArticleId IdType="pubmed">26484181</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>F1000Res. 2016 Jul 28;5:1881</Citation>
<ArticleIdList><ArticleId IdType="pubmed">27610223</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>BMC Bioinformatics. 2010 Mar 08;11:119</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20211023</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Genome Res. 2012 Mar;22(3):557-67</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22147368</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Bioinformatics. 2016 Apr 1;32(7):1088-90</Citation>
<ArticleIdList><ArticleId IdType="pubmed">26614127</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>Front Microbiol. 2019 Jan 24;9:3349</Citation>
<ArticleIdList><ArticleId IdType="pubmed">30733714</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
</PubmedData>
</pubmed>
</record>
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