BEREN: a bioinformatic tool for recovering giant viruses, polinton-like viruses, and virophages in metagenomic data.

Motivation: Viruses in the kingdom Bamfordvirae, specifically giant viruses (NCLDVs) in the phylum Nucleocytoviricota and smaller members in the Preplasmiviricota phylum, are widespread and important groups of viruses that infect eukaryotes. While viruses in this kingdom, such as giant viruses, polinton-like viruses, and virophages, have gained large interest from researchers in recent years, there is still a lack of streamlined tools for the recovery of their genomes from metagenomic datasets. Results: Here, we present, BEREN, a comprehensive bioinformatic tool to unlock the diversity of these viruses in metagenomes through five modules for NCLDV genome, contig, and marker gene recovery, metabolic protein annotation, and Preplasmiviricota genome identification and annotation. BEREN's performance was benchmarked against other mainstream virus recovery tools using a mock metagenome, demonstrating superior recovery rates of NCLDV contigs and Preplasmiviricota genomes. Overall, BEREN offers a user-friendly, transparent bioinformatic solution for studying the ecological and functional roles of these eukaryotic viruses, facilitating broader access to their metagenomic analysis. Availability and implementation: BEREN is available at https://gitlab.com/benminch1/BEREN, and results from testing BEREN on a real-world metagenome are available in the Supplementary Files.