Whokaryote: distinguishing eukaryotic and prokaryotic contigs in metagenomes based on gene structure.

ABSTRACT: Metagenomics has become a prominent technology to study the functional potential of all organisms in a microbial community. Most studies focus on the bacterial content of these communities, while ignoring eukaryotic microbes. Indeed, many metagenomics analysis pipelines silently assume that all contigs in a metagenome are prokaryotic, likely resulting in less accurate annotation of eukaryotes in metagenomes. Early detection of eukaryotic contigs allows for eukaryote-specific gene prediction and functional annotation. Here, we developed a classifier that distinguishes eukaryotic from prokaryotic contigs based on foundational differences between these taxa in terms of gene structure. We first developed Whokaryote, a random forest classifier that uses intergenic distance, gene density and gen

SUBMITTER: Pronk LJU 

PROVIDER: S-EPMC9465069 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature