Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome.

ABSTRACT: Microbiome analysis is quickly moving towards high-throughput methods such as metagenomic sequencing. Accurate taxonomic classification of metagenomic data relies on reference sequence databases, and their associated taxonomy. However, for understudied environments such as the rumen microbiome many sequences will be derived from novel or uncultured microbes that are not present in reference databases. As a result, taxonomic classification of metagenomic data from understudied environments may be inaccurate. To assess the accuracy of taxonomic read classification, this study classified metagenomic data that had been simulated from cultured rumen microbial genomes from the Hungate collection. To assess the impact of reference databases on the accuracy of taxonomic classification, the data wa

SUBMITTER: Smith RH 

PROVIDER: S-EPMC9673341 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature