Benchmarking taxonomic classifiers with Illumina and Nanopore sequence data for clinical metagenomic diagnostic applications.

ABSTRACT: Culture-independent metagenomic detection of microbial species has the potential to provide rapid and precise real-time diagnostic results. However, it is potentially limited by sequencing and taxonomic classification errors. We use simulated and real-world data to benchmark rates of species misclassification using 100 reference genomes for each of the ten common bloodstream pathogens and six frequent blood-culture contaminants (n=1568, only 68 genomes were available for Micrococcus luteus). Simulating both with and without sequencing error for both the Illumina and Oxford Nanopore platforms, we evaluated commonly used classification tools including Kraken2, Bracken and Centrifuge, utilizing mini (8 GB) and standard (30-50 GB) databases. Bracken with the standard database per

SUBMITTER: Govender KN 

PROVIDER: S-EPMC9676057 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature