Galba: genome annotation with miniprot and AUGUSTUS
Tomáš Brůna1, Heng Li2,3, Joseph Guhlin4
1U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
BMC Bioinformatics
|August 31, 2023
Summary
GALBA is a new automated pipeline for accurate gene annotation in eukaryotic genomes. It addresses the need for better protein-coding gene identification, especially in large vertebrate genomes.
Area of Science:
- Genomics
- Bioinformatics
Background:
- The Earth Biogenome Project has expanded eukaryotic genome availability.
- Most new genomes lack protein-coding gene annotations, hindering research.
- Transcriptome data is absent for some sequenced genomes.
Purpose of the Study:
- To introduce GALBA, a novel automated pipeline for high-accuracy gene annotation.
- To address the limitations of existing gene annotation tools.
- To facilitate genome annotation for diverse eukaryotic organisms.
Main Methods:
- GALBA utilizes miniprot (a rapid protein-to-genome aligner) and AUGUSTUS.
- The pipeline is fully automated for efficient gene prediction.
- It is available as an open-source Docker image for high-performance computing.
Main Results:
- GALBA demonstrates high accuracy in gene prediction.
- The pipeline shows particular strength in annotating large vertebrate genomes.
- Successful use cases include insects, vertebrates, and a land plant.
Conclusions:
- GALBA meets the critical need for accurate gene annotation in new genomes.
- The pipeline is expected to significantly aid genome annotation efforts.
- Its open-source nature and ease of use promote broad adoption.
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