ArticleBMC bioinformatics2023
Galba: genome annotation with miniprot and AUGUSTUS.
Article in BMC bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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64 citing papers in PubMed.
- Combining Annotation Software to Identify Orthologous Genes (CASIO) Provides a New Dataset of Orthologous Genes for Swallowtail Butterflies.Molecular ecology resources · 2026Article
- The origin of the octoploid cloudberry (Rubus chamaemorus) genome is the result of multiple and complex polyploidization events.The Journal of heredity · 2026Article
- Chromosomal fusions shaped the genome of the greater hornwrack bryozoan (Flustra foliacea) (Linnaeus, 1758).The Journal of heredity · 2026Article
- Population genomics of yellow-eyed penguins uncovers subspecies divergence and candidate genes linked to respiratory distress syndrome.Nature ecology & evolution · 2026Article
- Loss of Major Histocompatibility Complex I and II Function in the Genome of Glacier Lanternfish Provides Insight Into Evolution of Vertebrate Immune Systems.Genome biology and evolution · 2026Article
- Centromeric satellite expansion drives genome evolution in the snowy owl.Genome biology · 2026Article
- De novo genome assemblies of threatened Asian hornbills (Bucerotidae) reveal declining population trajectories during the late Pleistocene.BMC ecology and evolution · 2026Article
- Telomere-to-telomere genome of Stylosanthes guianensis uncovers symbiotic adaptation to phosphorus-deficient soils.Genome biology · 2026Article
- Long-term small effective population size, inbreeding, and a recessive lethal haplotype drive premature death in the endangered Devils Hole pupfish (bioRxiv : the preprint server for biology · 2026Article
- Transcriptomic genotyping elucidates the population structure and demographic history of the endangered poison frog Oophaga vicentei (Anura: Dendrobatidae).BMC genomics · 2026Article
- Chromosome-level de novo assembly of the nuclear and mitochondrial genomes of Arcopilus aureus, a filamentous fungus with multifaceted ecological and economic roles.Scientific data · 2026Article
- Chromosome-level genome assembly of Norwegian wild alpine reindeer (Rangifer tarandus tarandus).The Journal of heredity · 2026Article
- Haplotype-resolved genome of Citrus × sinensis 'Pera IAC', the most widely cultivated sweet orange in Brazil.Scientific data · 2026Article
- Rapid mid-Cretaceous diversification of squid and cuttlefish preceded radiation into coastal niches.Nature ecology & evolution · 2026Article
- Genomic Divergence BetweenEcology and evolution · 2026Article
- Evolutionary and methodological considerations when interpreting gene presence-absence variation in pangenomes.NAR genomics and bioinformatics · 2026Review
- Near telomere-to-telomere genome assembly of the stone loach (Traccatichthys pulcher).Scientific data · 2026Article
- Rapid genome modifications including chromosomal fusions and large-scale inversions are key features in Arctic codfish species.Genome biology · 2026Article
- Whole-genome assembly and annotation of the acorn weevil, Curculio nanulus (Coleoptera: Curculionidae).G3 (Bethesda, Md.) · 2026Article
- Comparative gene annotation and orthology assignments across 301 species of Drosophilidae.bioRxiv : the preprint server for biology · 2026Article
4 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
Funding
Abstract
backgroundThe 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.
resultsVarious 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.
conclusionsOur 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.
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