Efficient and Quality-Optimized Metagenomic Pipeline Designed for Taxonomic Classification in Routine Microbiological Clinical Tests.

ABSTRACT: Metagenomics analysis is now routinely used for clinical diagnosis in several diseases, and we need confidence in interpreting metagenomics analysis of microbiota. Particularly from the side of clinical microbiology, we consider that it would be a major milestone to further advance microbiota studies with an innovative and significant approach consisting of processing steps and quality assessment for interpreting metagenomics data used for diagnosis. Here, we propose a methodology for taxon identification and abundance assessment of shotgun sequencing data of microbes that are well fitted for clinical setup. Processing steps of quality controls have been developed in order (i) to avoid low-quality reads and sequences, (ii) to optimize abundance thresholds and profiles, (iii) to combine cla

SUBMITTER: Buffet-Bataillon S 

PROVIDER: S-EPMC9026403 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature