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, scalable Nextflow pipeline for prokaryotic genome annotation that identifies coding and noncoding regions, predicts protein functions, including antimicrobial resistance, and delineates gene clusters. The pipeline summarizes these results in a GFF (General Feature Format) file that can be easily utilized in downstream analysis or visualized using common genome browsers. Here, we show how it works on 200 genomes from 29 prokaryotic phyla, including isolate genomes and known and novel 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.

During collaborative writing each author works on a copy of the shared document. These copies are then merged to produce the final document. This asynchronous work is supported by several collaborative writing tools. While these tools are excellent at merging and detecting syntactic conflicts, they are not able to easily recognise semantic inconsistencies. This hinders the coherence of the document because while each individual copy might be well constructed, they may not be after the merge. To address this, we investigate the combination of the Rhetorical Structure Theory with Operational Transformation approach. In this paper, we define a data model, a set of operations to manipulate the RST structures and a set of transformation functions. A validity checker alerts the authors to areas in the text with possible semantic lapses in the merged documents.