Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities
Identifieur interne : 000117 ( Main/Exploration ); précédent : 000116; suivant : 000118Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities
Auteurs : Michael A. Peabody ; Thea Van Rossum ; Raymond Lo ; Fiona S. L. BrinkmanSource :
- BMC Bioinformatics [ 1471-2105 ] ; 2015.
Abstract
The field of metagenomics (study of genetic material recovered directly from an environment) has grown rapidly, with many bioinformatics analysis methods being developed. To ensure appropriate use of such methods, robust comparative evaluation of their accuracy and features is needed. For taxonomic classification of sequence reads, such evaluation should include use of clade exclusion, which better evaluates a method’s accuracy when identical sequences are not present in any reference database, as is common in metagenomic analysis. To date, relatively small evaluations have been performed, with evaluation approaches like clade exclusion limited to assessment of new methods by the authors of the given method. What is needed is a rigorous, independent comparison between multiple major methods, using the same
An overview of the features of 38 bioinformatics methods is provided, evaluating accuracy with a focus on 11 programs that have reference databases that can be modified and therefore most robustly evaluated with clade exclusion. Taxonomic classification of sequence reads was evaluated using both
The accuracy of shotgun metagenomics classification methods varies widely. No one program clearly outperformed others in all evaluation scenarios; rather, the results illustrate the strengths of different methods for different purposes. Researchers must appreciate method differences, choosing the program best suited for their particular analysis to avoid very misleading results. Use of standardized datasets for method comparisons is encouraged, as is use of mock microbial community controls suitable for a particular metagenomic analysis.
The online version of this article (doi:10.1186/s12859-015-0788-5) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12859-015-0788-5
PubMed: 26537885
PubMed Central: 4634789
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Evaluation of shotgun metagenomics sequence classification methods using <italic>in silico</italic> and <italic>in vitro</italic> simulated communities</title><author><name sortKey="Peabody, Michael A" sort="Peabody, Michael A" uniqKey="Peabody M" first="Michael A." last="Peabody">Michael A. Peabody</name><affiliation><nlm:aff id="Aff1">Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC Canada</nlm:aff><wicri:noCountry code="subfield">BC Canada</wicri:noCountry></affiliation></author><author><name sortKey="Van Rossum, Thea" sort="Van Rossum, Thea" uniqKey="Van Rossum T" first="Thea" last="Van Rossum">Thea Van Rossum</name><affiliation><nlm:aff id="Aff1">Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC Canada</nlm:aff><wicri:noCountry code="subfield">BC Canada</wicri:noCountry></affiliation></author><author><name sortKey="Lo, Raymond" sort="Lo, Raymond" uniqKey="Lo R" first="Raymond" last="Lo">Raymond Lo</name><affiliation><nlm:aff id="Aff1">Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC Canada</nlm:aff><wicri:noCountry code="subfield">BC Canada</wicri:noCountry></affiliation></author><author><name sortKey="Brinkman, Fiona S L" sort="Brinkman, Fiona S L" uniqKey="Brinkman F" first="Fiona S. L." last="Brinkman">Fiona S. L. Brinkman</name><affiliation><nlm:aff id="Aff1">Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC Canada</nlm:aff><wicri:noCountry code="subfield">BC Canada</wicri:noCountry></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26537885</idno><idno type="pmc">4634789</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4634789</idno><idno type="RBID">PMC:4634789</idno><idno type="doi">10.1186/s12859-015-0788-5</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000159</idno><idno type="wicri:Area/Pmc/Curation">000159</idno><idno type="wicri:Area/Pmc/Checkpoint">000109</idno><idno type="wicri:Area/Ncbi/Merge">000684</idno><idno type="wicri:Area/Ncbi/Curation">000684</idno><idno type="wicri:Area/Ncbi/Checkpoint">000684</idno><idno type="wicri:Area/Main/Merge">000117</idno><idno type="wicri:Area/Main/Curation">000117</idno><idno type="wicri:Area/Main/Exploration">000117</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Evaluation of shotgun metagenomics sequence classification methods using <italic>in silico</italic> and <italic>in vitro</italic> simulated communities</title><author><name sortKey="Peabody, Michael A" sort="Peabody, Michael A" uniqKey="Peabody M" first="Michael A." last="Peabody">Michael A. Peabody</name><affiliation><nlm:aff id="Aff1">Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC Canada</nlm:aff><wicri:noCountry code="subfield">BC Canada</wicri:noCountry></affiliation></author><author><name sortKey="Van Rossum, Thea" sort="Van Rossum, Thea" uniqKey="Van Rossum T" first="Thea" last="Van Rossum">Thea Van Rossum</name><affiliation><nlm:aff id="Aff1">Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC Canada</nlm:aff><wicri:noCountry code="subfield">BC Canada</wicri:noCountry></affiliation></author><author><name sortKey="Lo, Raymond" sort="Lo, Raymond" uniqKey="Lo R" first="Raymond" last="Lo">Raymond Lo</name><affiliation><nlm:aff id="Aff1">Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC Canada</nlm:aff><wicri:noCountry code="subfield">BC Canada</wicri:noCountry></affiliation></author><author><name sortKey="Brinkman, Fiona S L" sort="Brinkman, Fiona S L" uniqKey="Brinkman F" first="Fiona S. L." last="Brinkman">Fiona S. L. Brinkman</name><affiliation><nlm:aff id="Aff1">Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC Canada</nlm:aff><wicri:noCountry code="subfield">BC Canada</wicri:noCountry></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The field of metagenomics (study of genetic material recovered directly from an environment) has grown rapidly, with many bioinformatics analysis methods being developed. To ensure appropriate use of such methods, robust comparative evaluation of their accuracy and features is needed. For taxonomic classification of sequence reads, such evaluation should include use of clade exclusion, which better evaluates a method’s accuracy when identical sequences are not present in any reference database, as is common in metagenomic analysis. To date, relatively small evaluations have been performed, with evaluation approaches like clade exclusion limited to assessment of new methods by the authors of the given method. What is needed is a rigorous, independent comparison between multiple major methods, using the same <italic>in silico</italic> and <italic>in vitro</italic> test datasets, with and without approaches like clade exclusion, to better characterize accuracy under different conditions.</p></sec><sec><title>Results</title><p>An overview of the features of 38 bioinformatics methods is provided, evaluating accuracy with a focus on 11 programs that have reference databases that can be modified and therefore most robustly evaluated with clade exclusion. Taxonomic classification of sequence reads was evaluated using both <italic>in silico</italic> and <italic>in vitro</italic> mock bacterial communities. Clade exclusion was used at taxonomic levels from species to class—identifying how well methods perform in progressively more difficult scenarios. A wide range of variability was found in the sensitivity, precision, overall accuracy, and computational demand for the programs evaluated. In experiments where distilled water was spiked with only 11 bacterial species, frequently dozens to hundreds of species were falsely predicted by the most popular programs. The different features of each method (forces predictions or not, etc.) are summarized, and additional analysis considerations discussed.</p></sec><sec><title>Conclusions</title><p>The accuracy of shotgun metagenomics classification methods varies widely. No one program clearly outperformed others in all evaluation scenarios; rather, the results illustrate the strengths of different methods for different purposes. Researchers must appreciate method differences, choosing the program best suited for their particular analysis to avoid very misleading results. Use of standardized datasets for method comparisons is encouraged, as is use of mock microbial community controls suitable for a particular metagenomic analysis.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12859-015-0788-5) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Wooley, Jc" uniqKey="Wooley J">JC Wooley</name></author><author><name sortKey="Godzik, A" uniqKey="Godzik A">A Godzik</name></author><author><name sortKey="Friedberg, I" uniqKey="Friedberg I">I Friedberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Handelsman, J" uniqKey="Handelsman J">J Handelsman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Acinas, Sg" uniqKey="Acinas S">SG Acinas</name></author><author><name sortKey="Sarma Rupavtarm, R" 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sortKey="Kyrpides, Nc" uniqKey="Kyrpides N">NC Kyrpides</name></author><author><name sortKey="Ivanova, N" uniqKey="Ivanova N">N Ivanova</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mohammed, Mh" uniqKey="Mohammed M">MH Mohammed</name></author><author><name sortKey="Ghosh, Ts" uniqKey="Ghosh T">TS Ghosh</name></author><author><name sortKey="Reddy, Rm" uniqKey="Reddy R">RM Reddy</name></author><author><name sortKey="Reddy, Cvsk" uniqKey="Reddy C">CVSK Reddy</name></author><author><name sortKey="Singh, Nk" uniqKey="Singh N">NK Singh</name></author><author><name sortKey="Mande, Ss" uniqKey="Mande S">SS Mande</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rasheed, Z" uniqKey="Rasheed Z">Z Rasheed</name></author><author><name sortKey="Rangwala, H" uniqKey="Rangwala H">H Rangwala</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liu, J" uniqKey="Liu J">J Liu</name></author><author><name sortKey="Wang, H" uniqKey="Wang H">H Wang</name></author><author><name sortKey="Yang, H" uniqKey="Yang H">H Yang</name></author><author><name sortKey="Zhang, Y" uniqKey="Zhang Y">Y Zhang</name></author><author><name sortKey="Wang, J" uniqKey="Wang J">J Wang</name></author><author><name sortKey="Zhao, F" uniqKey="Zhao F">F Zhao</name></author><author><name sortKey="Qi, J" uniqKey="Qi J">J Qi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yu, F" uniqKey="Yu F">F Yu</name></author><author><name sortKey="Sun, Y" uniqKey="Sun Y">Y Sun</name></author><author><name sortKey="Liu, L" uniqKey="Liu L">L Liu</name></author><author><name sortKey="Farmerie, W" uniqKey="Farmerie W">W Farmerie</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list></list><tree><noCountry><name sortKey="Brinkman, Fiona S L" sort="Brinkman, Fiona S L" uniqKey="Brinkman F" first="Fiona S. L." last="Brinkman">Fiona S. L. Brinkman</name><name sortKey="Lo, Raymond" sort="Lo, Raymond" uniqKey="Lo R" first="Raymond" last="Lo">Raymond Lo</name><name sortKey="Peabody, Michael A" sort="Peabody, Michael A" uniqKey="Peabody M" first="Michael A." last="Peabody">Michael A. Peabody</name><name sortKey="Van Rossum, Thea" sort="Van Rossum, Thea" uniqKey="Van Rossum T" first="Thea" last="Van Rossum">Thea Van Rossum</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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