RAGNAROK (RApid GeNe Annotation ROcKs)

RAGNAROK integrates ab initio prediction, transcriptome and protein evidence, repeat annotation, functional assignment, and quality assessment into a single reproducible workflow for rapid and accurate genome annotation of plant and other eukaryotic genomes.

Key Features:

• GPU Acceleration: RAGNAROK utilizes GPU acceleration and parallelization to improve runtime performance and scalability from small to gigabase-scale genomes.
• Modular Architecture: The pipeline is built on Nextflow and Apptainer with a modular design that integrates multiple annotation methods into a reproducible workflow.
• Benchmarking Performance: RAGNAROK achieved higher sensitivity, precision, and F1 scores at the exon, transcript, and gene levels compared to BRAKER3 across five diverse plant genomes.
• Re-annotation Improvement: RAGNAROK improved BUSCO completeness scores, produced more ideal mono:multi-exonic gene ratios, and reduced missing gene content compared to MAKER-annotated Rosaceae genomes.

Scientific Applications:

• De Novo Genome Annotation: RAGNAROK enables rapid and accurate gene annotation for newly assembled plant genomes using integrated evidence-based and ab initio approaches.
• Genome Re-annotation: RAGNAROK improves existing annotations by re-annotating previously annotated genomes with higher completeness and accuracy, as demonstrated with Rosaceae species.
• Pangenome Annotation: RAGNAROK supports annotation of high-quality genome assemblies and pangenomes enabled by third-generation sequencing technologies.
• Eukaryotic Genome Extension: The pipeline's modular design and workflow scalability provide a foundation for extending annotation capabilities to animal, fungal, and other eukaryotic genomes.

Methodology:

RAGNAROK is built on Nextflow and Apptainer and integrates ab initio prediction, transcriptome and protein evidence, repeat annotation, functional assignment, and quality assessment into a single workflow with GPU acceleration and parallelization.