Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities.

ABSTRACT: Taxonomic classification is crucial in identifying organisms within diverse microbial communities when using metagenomics shotgun sequencing. While second-generation Illumina sequencing still dominates, third-generation nanopore sequencing promises improved classification through longer reads. However, extensive benchmarking studies on nanopore data are lacking. We systematically evaluated performance of bacterial taxonomic classification for metagenomics nanopore sequencing data for several commonly used classifiers, using standardized reference sequence databases, on the largest collection of publicly available data for defined mock communities thus far (nine samples), representing different research domains and application scopes. Our results categorize classifiers into three categories

SUBMITTER: Van Uffelen A 

PROVIDER: S-EPMC11316826 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature