GALBA: Genome Annotation with Miniprot and AUGUSTUS

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• The Earth Biogenome Project has accelerated eukaryotic genome sequencing, yet many lack essential protein-coding gene annotations.
• Existing gene annotation tools have limitations, hindering comprehensive genomic analysis.

Approach:

• We developed GALBA, a fully automated pipeline for high-accuracy gene prediction.
• GALBA integrates miniprot, a fast protein-to-genome aligner, with AUGUSTUS for robust gene prediction.

Key Points:

• GALBA demonstrates high accuracy, particularly for large vertebrate genomes.
• The pipeline was successfully applied to insects, vertebrates, and an unannotated land plant.
• It is open-source, available as a Docker image for easy deployment on high-performance computing environments.

Conclusions:

• GALBA addresses the urgent need for accurate gene annotation in newly sequenced eukaryotic genomes.
• This tool is expected to significantly advance genome annotation across diverse species.