mettannotator

mettannotator annotates prokaryotic genomes by identifying coding and noncoding regions, predicting protein functions including antimicrobial resistance, and delineating gene clusters in both well-described and novel taxa at scale.

Key Features:

• Coding and Noncoding Region Identification: The pipeline identifies both coding and noncoding regions in prokaryotic genome assemblies.
• Protein Function Prediction: It predicts protein functions, including antimicrobial resistance.
• Gene Cluster Delineation: It delineates gene clusters in annotated genomes.
• Integrated GFF Output: It generates a GFF (General Feature Format) file summarizing results from multiple tools for downstream analysis and visualization.
• Scalability: It processes large datasets, as demonstrated on 200 genomes from 29 prokaryotic phyla including isolate genomes and metagenome-assembled genomes.

Scientific Applications:

• Prokaryotic Genome Annotation: It annotates genomes from both isolated organisms and environmental samples, including novel species poorly represented in reference databases.
• Metagenome-Assembled Genome Analysis: It annotates known and novel metagenome-assembled genomes across diverse prokaryotic phyla.
• Antimicrobial Resistance Detection: It identifies antimicrobial resistance functions in prokaryotic genomes.
• Comparative Genomics: The GFF output enables downstream analysis and visualization in common genome browsers.

Methodology:

The pipeline is written in Nextflow and Python, integrates multiple annotation tools, and summarizes their results in a GFF file.