Impact of simulation and reference catalogues on the evaluation of taxonomic profiling pipelines.

ABSTRACT: Microbiome profiling tools rely on reference catalogues, which significantly affect their performance. Comparing them is, however, challenging, mainly due to differences in their native catalogues. In this study, we present a novel standardized benchmarking framework that makes such comparisons more accurate. We decided not to customize databases but to translate results to a common reference to use the tools with their native environment. Specifically, we conducted two realistic simulations of gut microbiome samples, each based on a specific taxonomic profiler, and used two different taxonomic references to project their results, namely the Genome Taxonomy Database and the Unified Human Gastrointestinal Genome. To demonstrate the importance of using such a framework, we evaluated four est

SUBMITTER: Puller V 

PROVIDER: S-EPMC11728698 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature