TY - JOUR T1 - eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale JF - bioRxiv DO - 10.1101/2021.06.03.446934 SP - 2021.06.03.446934 AU - Carlos P. Cantalapiedra AU - Ana Hernández-Plaza AU - Ivica Letunic AU - Peer Bork AU - Jaime Huerta-Cepas Y1 - 2021/01/01 UR - http://biorxiv.org/content/early/2021/06/04/2021.06.03.446934.abstract N2 - Even though automated functional annotation of genes represents a fundamental step in most genomic and metagenomic workflows, it remains challenging at large scales. Here, we describe a major upgrade to eggNOG-mapper, a tool for functional annotation based on precomputed orthology assignments, now optimized for vast (meta)genomic data sets. Improvements in version 2 include a full update of both the genomes and functional databases to those from eggNOG v5, as well as several efficiency enhancements and new features. Most notably, eggNOG-mapper v2 now allows: (i) de novo gene prediction from raw contigs, (ii) built-in pairwise orthology prediction, (iii) fast protein domain discovery, and (iv) automated GFF decoration. eggNOG-mapper v2 is available as a standalone tool or as an online service at http://eggnog-mapper.embl.de.Competing Interest StatementThe authors have declared no competing interest. ER -