MicrobeAnnotator: a user-friendly, comprehensive microbial genome annotation pipeline

Abstract

SummaryHigh-throughput sequencing has increased the number of microbial genomes from isolates, single cells, and metagenomes available. To analyze and compare these genomes, fast and comprehensive annotation pipelines are needed. Although several approaches exist for genome annotation, these are typically not designed for easy incorporation into analysis pipelines, do not combine results from several annotation databases or offer easy-to-use summaries of metabolic reconstructions in a high-throughput mode. Here, we introduce MicrobeAnnotator, a fully automated pipeline for the comprehensive annotation of microbial genomes that combines results from several reference protein databases to reliably summarize the metabolic potential of the genomes based on KEGG modules. AvailabilityMicrobeAnnotator is implemented in Python and is freely available under an open source Artistic Licence 2.0 from https://github.com/cruizperez/MicrobeAnnotator Contactcruizperez3@gatech.edu; kostas@ce.gatech.edu