Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics.

ABSTRACT: 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 metagenomics 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,

SUBMITTER: Siegwald L 

PROVIDER: S-EPMC5215245 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature