The META tool optimizes metagenomic analyses across sequencing platforms and classifiers

A major challenge in the field of metagenomics is the selection of the correct combination of sequencing platform and downstream metagenomic analysis algorithm, or "classifier". Here, we present the Metagenomic Evaluation Tool Analyzer (META), which produces simulated data and facilitates...

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Published in:Frontiers in bioinformatics Vol. 2; p. 969247
Main Authors: Player, Robert A, Aguinaldo, Angeline M, Merritt, Brian B, Maszkiewicz, Lisa N, Adeyemo, Oluwaferanmi E, Forsyth, Ellen R, Verratti, Kathleen J, Chee, Brant W, Grady, Sarah L, Bradburne, Christopher E
Format: Journal Article
Language:English
Published: Switzerland Frontiers Media S.A 06-01-2023
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Summary:A major challenge in the field of metagenomics is the selection of the correct combination of sequencing platform and downstream metagenomic analysis algorithm, or "classifier". Here, we present the Metagenomic Evaluation Tool Analyzer (META), which produces simulated data and facilitates platform and algorithm selection for any given metagenomic use case. META-generated read data are modular, scalable, and reflect user-defined community profiles, while the downstream analysis is done using a variety of metagenomic classifiers. Reported results include information on resource utilization, time-to-answer, and performance. Real-world data can also be analyzed using selected classifiers and results benchmarked against simulations. To test the utility of the META software, simulated data was compared to real-world viral and bacterial metagenomic samples run on four different sequencers and analyzed using 12 metagenomic classifiers. Lastly, we introduce "META Score": a unified, quantitative value which rates an analytic classifier's ability to both identify and count taxa in a representative sample.
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Nicolás Pinel, EAFIT University, Colombia
This article was submitted to Protein Bioinformatics, a section of the journal Frontiers in Bioinformatics
Edited by: Mindaugas Margelevicius, Vilnius University, Lithuania
Jose Manuel Martí, Lawrence Livermore National Laboratory (DOE), United States
Reviewed by: Annelies Kroneman, National Institute for Public Health and the Environment, Netherlands
ISSN:2673-7647
2673-7647
DOI:10.3389/fbinf.2022.969247