Gauge your phage: benchmarking of bacteriophage identification tools in metagenomic sequencing data.

ABSTRACT:

Background

The prediction of bacteriophage sequences in metagenomic datasets has become a topic of considerable interest, leading to the development of many novel bioinformatic tools. A comparative analysis of ten state-of-the-art phage identification tools was performed to inform their usage in microbiome research.

Methods

Artificial contigs generated from complete RefSeq genomes representing phages, plasmids, and chromosomes, and a previously sequenced mock community containing four phage species, were used to evaluate the precision, recall, and F1 scores of the tools. We also generated a dataset of randomly shuffled sequences to quantify false-positive calls. In addition, a set of previously simulated viromes was used to assess diversity bias in each tool's output.

Res

SUBMITTER: Ho SFS 

PROVIDER: S-EPMC10120246 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature