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Galba: genome annotation with miniprot and AUGUSTUS.
- Source :
-
BMC bioinformatics [BMC Bioinformatics] 2023 Aug 31; Vol. 24 (1), pp. 327. Date of Electronic Publication: 2023 Aug 31. - Publication Year :
- 2023
-
Abstract
- 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.<br />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.<br />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.<br /> (© 2023. BioMed Central Ltd., part of Springer Nature.)
- Subjects :
- Animals
Molecular Sequence Annotation
Transcriptome
Eukaryota
Eukaryotic Cells
Subjects
Details
- Language :
- English
- ISSN :
- 1471-2105
- Volume :
- 24
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- BMC bioinformatics
- Publication Type :
- Academic Journal
- Accession number :
- 37653395
- Full Text :
- https://doi.org/10.1186/s12859-023-05449-z