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Galba: genome annotation with miniprot and AUGUSTUS
- Background The Earth Biogenome Project has rapidly increased the number of available eukaryotic genomes, but most released genomes continue to lack annotation of protein-coding genes. In addition, no transcriptome data is available for some genomes. Results Various gene annotation tools have been developed but each has its limitations. Here, we introduce GALBA, a fully automated pipeline that utilizes miniprot, a rapid protein-to-genome aligner, in combination with AUGUSTUS to predict genes with high accuracy. Accuracy results indicate that GALBA is particularly strong in the annotation of large vertebrate genomes. We also present use cases in insects, vertebrates, and a land plant. GALBA is fully open source and available as a docker image for easy execution with Singularity in high-performance computing environments. Conclusions Our pipeline addresses the critical need for accurate gene annotation in newly sequenced genomes, and we believe that GALBA will greatly facilitate genome annotation for diverse organisms.
Author: | Tomáš Brůna, Heng Li, Joseph Guhlin, Daniel Honsel, Steffen Herbold, Mario Stanke, Natalia Nenasheva, Matthis Ebel, Lars Gabriel, Katharina J. Hoff |
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URN: | urn:nbn:de:gbv:9-opus-106573 |
DOI: | https://doi.org/10.1186/s12859-023-05449-z |
ISSN: | 1471-2105 |
Parent Title (English): | BMC Bioinformatics |
Publisher: | BioMed Central (BMC) |
Place of publication: | London |
Document Type: | Article |
Language: | English |
Date of first Publication: | 2023/08/31 |
Release Date: | 2024/02/19 |
Tag: | AUGUSTUS; Gene prediction; Miniprot; Protein coding gene |
Volume: | 24 |
Article Number: | 327 |
Page Number: | 21 |
Faculties: | Mathematisch-Naturwissenschaftliche Fakultät / Institut für Mathematik und Informatik |
Collections: | Artikel aus DFG-gefördertem Publikationsfonds |
Licence (German): | Creative Commons - Namensnennung 4.0 International |