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

Area of Science:

• Genomics
• Bioinformatics
• Microbial Ecology

Background:

• Increasing numbers of prokaryotic genome assemblies from isolates and environmental samples present challenges for annotation.
• Novel species are often poorly represented in existing reference databases, necessitating advanced annotation tools.

Purpose of the Study:

• To introduce mettannotator, a comprehensive and scalable Nextflow pipeline for prokaryotic genome annotation.
• To enable annotation of both well-described and novel prokaryotic taxa at scale.

Main Methods:

• The mettannotator pipeline is implemented in Nextflow and Python.
• It identifies coding and noncoding regions, predicts protein functions (including antimicrobial resistance), and delineates gene clusters.
• Results are summarized in a General Feature Format (GFF) file.

Main Results:

• The pipeline was tested on 200 genomes from 29 prokaryotic phyla, including isolate and metagenome-assembled genomes.
• Performance metrics were generated and compared against other annotation tools.
• The tool successfully annotates diverse prokaryotic genomes, including novel taxa.

Conclusions:

• Mettannotator provides a robust and scalable solution for prokaryotic genome annotation.
• The pipeline facilitates downstream analysis and visualization of genomic data.
• It addresses the need for efficient annotation of both known and novel prokaryotic species.