eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale

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• Cold Spring Harbor Laboratory (biorxiv.org)Accepted manuscript · PDF
• National Institutes of Health (ncbi.nlm.nih.gov)Published version · Web page
• Consejo Superior de Investigaciones Científicas (digital.csic.es)Preprint · PDF
• Consejo Superior de Investigaciones Científicas (hdl.handle.net)Preprint · Web page
• University of Würzburg (opus.bibliothek.uni-wuerzburg.de)Preprint · Web page

Abstract

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 for: 1) de novo gene prediction from raw contigs, 2) built-in pairwise orthology prediction, 3) fast protein domain discovery, and 4) automated GFF decoration. eggNOG-mapper v2 is available as a standalone tool or as an online service at http://eggnog-mapper.embl.de.