mettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies

Summary: In recent years there has been a surge in prokaryotic genome assemblies, coming from both isolated organisms and environmental samples. These assemblies often include novel species that are poorly represented in reference databases creating a need for a tool that can annotate both well-described and novel taxa, and can run at scale. Here, we present mettannotator - a comprehensive Nextflow pipeline for prokaryotic genome annotation that identifies coding and non-coding regions, predicts protein functions, including antimicrobial resistance, and delineates gene clusters. The pipeline summarises the results of these tools in a GFF (General Feature Format) file that can be easily utilised in downstream analysis or visualised using common genome browsers. Mettannotator has been tested on both novel and known taxa, and used across Ensembl Bacteria and MGnify. Here, we show how it works on 29 prokaryotic phyla, both isolate and metagenome-assembled genomes, and present metrics on its performance in comparison to other tools. Availability and implementation: The pipeline is written in Nextflow and Python and published under an open source Apache 2.0 licence. Instructions and source code can be accessed at https://github.com/EBI Metagenomics/mettannotator. The pipeline is also available on WorkflowHub: https://workflowhub.eu/workflows/1069.