Scipediacontent: Scipediacontent moved page Draft Content 138114072 to Hot et al 2017a

2021-02-15T09:34:40Z

Scipediacontent moved page Draft Content 138114072 to Hot et al 2017a

Scipediacontent: Created page with " == Abstract == International audience; Targeted metagenomics, also known as metagenetics, is a high-throughput sequencing application focusing on a nucleotide target in a mi..."

2021-02-15T09:34:37Z

Created page with " == Abstract == International audience; Targeted metagenomics, also known as metagenetics, is a high-throughput sequencing application focusing on a nucleotide target in a mi..."

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== Abstract ==

International audience; Targeted metagenomics, also known as metagenetics, is a high-throughput sequencing application focusing on a nucleotide target in a microbiome to describe its taxonomic content. A wide range of bioinformatics pipelines are available to analyze sequencing outputs, and the choice of an appropriate tool is crucial and not trivial. No standard evaluation method exists for estimating the accuracy of a pipeline for targeted metagenomics analyses. This article proposes an evaluation protocol containing real and simulated targeted metage-nomics datasets, and adequate metrics allowing us to study the impact of different variables on the biological interpretation of results. This protocol was used to compare six different bioinformatics pipelines in the basic user context: Three common ones (mothur, QIIME and BMP) based on a clustering-first approach and three emerging ones (Kraken, CLARK and One Codex) using an assignment-first approach. This study surprisingly reveals that the effect of sequencing errors has a bigger impact on the results that choosing different amplified regions. Moreover, increasing sequencing throughput increases richness overestima-tion, even more so for microbiota of high complexity. Finally, the choice of the reference database has a bigger impact on richness estimation for clustering-first pipelines, and on correct taxa identification for assignment-first pipelines. Using emerging assignment-first pipelines is a valid approach for targeted metagenomics analyses, with a quality of results comparable to popular clustering-first pipelines, even with an error-prone sequencing technology like Ion Torrent. However, those pipelines are highly sensitive to the quality of databases and their annotations, which makes clustering-first pipelines still the only reliable approach for studying microbiomes that are not well described.

Document type: Article

== Full document ==
<pdf>Media:Draft_Content_138114072-beopen757-4504-document.pdf</pdf>

== Original document ==

The different versions of the original document can be found in:

* [http://europepmc.org/articles/PMC5215245 http://europepmc.org/articles/PMC5215245]

* [http://hdl.handle.net/20.500.12210/24067 http://hdl.handle.net/20.500.12210/24067]

* [http://hdl.handle.net/20.500.12210/28882 http://hdl.handle.net/20.500.12210/28882]

* [https://doi.org/10.1371/journal.pone.0169563 https://doi.org/10.1371/journal.pone.0169563] under the license cc-by

* [http://dx.plos.org/10.1371/journal.pone.0169563 http://dx.plos.org/10.1371/journal.pone.0169563],
: [http://dx.doi.org/10.1371/journal.pone.0169563 http://dx.doi.org/10.1371/journal.pone.0169563] under the license http://creativecommons.org/licenses/by/4.0/

* [http://europepmc.org/articles/PMC5215245?pdf=render http://europepmc.org/articles/PMC5215245?pdf=render],
: [https://doaj.org/toc/1932-6203 https://doaj.org/toc/1932-6203]

* [https://hal.archives-ouvertes.fr/hal-01575755 https://hal.archives-ouvertes.fr/hal-01575755],
: [https://hal.archives-ouvertes.fr/hal-01575755/document https://hal.archives-ouvertes.fr/hal-01575755/document],
: [https://hal.archives-ouvertes.fr/hal-01575755/file/journal.pone.0169563.pdf https://hal.archives-ouvertes.fr/hal-01575755/file/journal.pone.0169563.pdf]

* [https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0169563 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0169563],
: [https://www.ncbi.nlm.nih.gov/pubmed/28052134 https://www.ncbi.nlm.nih.gov/pubmed/28052134],
: [https://hal.archives-ouvertes.fr/hal-01575755/document https://hal.archives-ouvertes.fr/hal-01575755/document],
: [https://hal.archives-ouvertes.fr/hal-01575755 https://hal.archives-ouvertes.fr/hal-01575755],
: [http://europepmc.org/abstract/MED/28052134 http://europepmc.org/abstract/MED/28052134],
: [https://ui.adsabs.harvard.edu/abs/2017PLoSO..1269563S/abstract https://ui.adsabs.harvard.edu/abs/2017PLoSO..1269563S/abstract],
: [https://dx.plos.org/10.1371/journal.pone.0169563 https://dx.plos.org/10.1371/journal.pone.0169563],
: [https://paperity.org/p/80231307/assessment-of-common-and-emerging-bioinformatics-pipelines-for-targeted-metagenomics https://paperity.org/p/80231307/assessment-of-common-and-emerging-bioinformatics-pipelines-for-targeted-metagenomics],
: [https://core.ac.uk/display/149652434 https://core.ac.uk/display/149652434],
: [https://academic.microsoft.com/#/detail/2570945670 https://academic.microsoft.com/#/detail/2570945670]

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Scipediacontent: Scipediacontent moved page Draft Content 138114072 to Hot et al 2017a

Scipediacontent: Created page with " == Abstract == International audience; Targeted metagenomics, also known as metagenetics, is a high-throughput sequencing application focusing on a nucleotide target in a mi..."