Galba: genome annotation with miniprot and AUGUSTUS

Brůna, Tomáš; Li, Heng; Guhlin, Joseph; Honsel, Daniel; Herbold, Steffen; Stanke, Mario; Nenasheva, Natalia; Ebel, Matthis; Gabriel, Lars; Hoff, Katharina J.

doi:10.1186/s12859-023-05449-z

Title: Galba: genome annotation with miniprot and AUGUSTUS

Journal Article · 31 August 2023 · BMC Bioinformatics

DOI: https://doi.org/10.1186/s12859-023-05449-z · OSTI ID:2470966

Brůna, Tomáš ^[1]; Li, Heng ^[2]; Guhlin, Joseph ^[3]; Honsel, Daniel ^[4]; Herbold, Steffen ^[5]; Stanke, Mario ^[6]; Nenasheva, Natalia ^[6]; Ebel, Matthis ^[6]; Gabriel, Lars ^[6]; Hoff, Katharina J. ^[6]

Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Dana-Farber Cancer Institute, Boston, MA (United States); Harvard Medical School, Boston, MA (United States)
University of Otago, Dunedin (New Zealand)
University of Göttingen (Germany)
University of Passau (Germany)
University of Greifswald (Germany)

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. 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. 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.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE; US National Institute of Health (NIH); German Research Foundation

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2470966

Journal Information:: BMC Bioinformatics, Journal Name: BMC Bioinformatics Journal Issue: 1 Vol. 24; ISSN 1471-2105

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

References (46)

Using Repeat Masker to Identify Repetitive Elements in Genomic Sequences Chen, Nansheng Current Protocols in Bioinformatics, Vol. 5, Issue 1 https://doi.org/10.1002/0471250953.bi0410s05	journal	March 2004
Genome Annotation and Curation Using MAKER and MAKER‐P Campbell, Michael S.; Holt, Carson; Moore, Barry Current Protocols in Bioinformatics, Vol. 48, Issue 1 https://doi.org/10.1002/0471250953.bi0411s48	journal	December 2014
Predicting Genes in Single Genomes with AUGUSTUS Hoff, Katharina J.; Stanke, Mario Current Protocols in Bioinformatics, Vol. 65, Issue 1 https://doi.org/10.1002/cpbi.57	journal	November 2018
BUSCO: Assessing Genomic Data Quality and Beyond Manni, Mosè; Berkeley, Matthew R.; Seppey, Mathieu Current Protocols, Vol. 1, Issue 12 https://doi.org/10.1002/cpz1.323	journal	December 2021
GeMoMa: Homology-Based Gene Prediction Utilizing Intron Position Conservation and RNA-seq Data Keilwagen, Jens; Hartung, Frank; Grau, Jan Methods in Molecular Biology https://doi.org/10.1007/978-1-4939-9173-0_9	book	January 2019
The Coix Genome Provides Insights into Panicoideae Evolution and Papery Hull Domestication Guo, Chao; Wang, Yanan; Yang, Aiguo Molecular Plant, Vol. 13, Issue 2 https://doi.org/10.1016/j.molp.2019.11.008	journal	February 2020
The draft chromosome-level genome assembly of tetraploid ground cherry (Prunus fruticosa Pall.) from long reads Wöhner, Thomas W.; Emeriewen, Ofere F.; Wittenberg, Alexander H. J. Genomics, Vol. 113, Issue 6 https://doi.org/10.1016/j.ygeno.2021.11.002	journal	November 2021
Fast and sensitive protein alignment using DIAMOND Buchfink, Benjamin; Xie, Chao; Huson, Daniel H. Nature Methods, Vol. 12, Issue 1 https://doi.org/10.1038/nmeth.3176	journal	November 2014
A beginner's guide to eukaryotic genome annotation Yandell, Mark; Ence, Daniel Nature Reviews Genetics, Vol. 13, Issue 5 https://doi.org/10.1038/nrg3174	journal	April 2012
A comparative genomics multitool for scientific discovery and conservation Nature, Vol. 587, Issue 7833 https://doi.org/10.1038/s41586-020-2876-6	journal	November 2020
Nanopore sequencing technology, bioinformatics and applications Wang, Yunhao; Zhao, Yue; Bollas, Audrey Nature Biotechnology, Vol. 39, Issue 11 https://doi.org/10.1038/s41587-021-01108-x	journal	November 2021
A de novo transcriptional atlas in Danaus plexippus reveals variability in dosage compensation across tissues Ranz, José M.; González, Pablo M.; Clifton, Bryan D. Communications Biology, Vol. 4, Issue 1 https://doi.org/10.1038/s42003-021-02335-3	journal	June 2021
Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies Patalano, Solenn; Vlasova, Anna; Wyatt, Chris Proceedings of the National Academy of Sciences, Vol. 112, Issue 45 https://doi.org/10.1073/pnas.1515937112	journal	October 2015
Earth BioGenome Project: Sequencing life for the future of life Lewin, Harris A.; Robinson, Gene E.; Kress, W. John Proceedings of the National Academy of Sciences, Vol. 115, Issue 17 https://doi.org/10.1073/pnas.1720115115	journal	April 2018
RepeatModeler2 for automated genomic discovery of transposable element families Flynn, Jullien M.; Hubley, Robert; Goubert, Clément Proceedings of the National Academy of Sciences, Vol. 117, Issue 17 https://doi.org/10.1073/pnas.1921046117	journal	April 2020
Standards recommendations for the Earth BioGenome Project Lawniczak, Mara K. N.; Durbin, Richard; Flicek, Paul Proceedings of the National Academy of Sciences, Vol. 119, Issue 4 https://doi.org/10.1073/pnas.2115639118	journal	January 2022
Protein-to-genome alignment with miniprot Li, Heng Bioinformatics, Vol. 39, Issue 1 https://doi.org/10.1093/bioinformatics/btad014	journal	January 2023
Using native and syntenically mapped cDNA alignments to improve de novo gene finding Stanke, Mario; Diekhans, Mark; Baertsch, Robert Bioinformatics, Vol. 24, Issue 5 https://doi.org/10.1093/bioinformatics/btn013	journal	January 2008
Direct mapping and alignment of protein sequences onto genomic sequence Gotoh, Osamu Bioinformatics, Vol. 24, Issue 21 https://doi.org/10.1093/bioinformatics/btn460	journal	August 2008
BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1. Hoff, Katharina J.; Lange, Simone; Lomsadze, Alexandre Bioinformatics, Vol. 32, Issue 5 https://doi.org/10.1093/bioinformatics/btv661	journal	November 2015
GeneValidator: identify problems with protein-coding gene predictions Drăgan, Monica-Andreea; Moghul, Ismail; Priyam, Anurag Bioinformatics, Vol. 32, Issue 10 https://doi.org/10.1093/bioinformatics/btw015	journal	January 2016
NCBI Taxonomy: a comprehensive update on curation, resources and tools Schoch, Conrad L.; Ciufo, Stacy; Domrachev, Mikhail Database, Vol. 2020 https://doi.org/10.1093/database/baaa062	journal	January 2020
Tandem repeats finder: a program to analyze DNA sequences Benson, G. Nucleic Acids Research, Vol. 27, Issue 2 https://doi.org/10.1093/nar/27.2.573	journal	January 1999
The Sequence Read Archive: a decade more of explosive growth Katz, Kenneth; Shutov, Oleg; Lapoint, Richard Nucleic Acids Research, Vol. 50, Issue D1 https://doi.org/10.1093/nar/gkab1053	journal	November 2021
OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity Kuznetsov, Dmitry; Tegenfeldt, Fredrik; Manni, Mosè Nucleic Acids Research, Vol. 51, Issue D1 https://doi.org/10.1093/nar/gkac998	journal	November 2022
Gene identification in novel eukaryotic genomes by self-training algorithm Lomsadze, A. Nucleic Acids Research, Vol. 33, Issue 20 https://doi.org/10.1093/nar/gki937	journal	November 2005
Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features Iwata, Hiroaki; Gotoh, Osamu Nucleic Acids Research, Vol. 40, Issue 20 https://doi.org/10.1093/nar/gks708	journal	July 2012
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation O'Leary, Nuala A.; Wright, Mathew W.; Brister, J. Rodney Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1189	journal	November 2015
Using intron position conservation for homology-based gene prediction Keilwagen, Jens; Wenk, Michael; Erickson, Jessica L. Nucleic Acids Research, Vol. 44, Issue 9 https://doi.org/10.1093/nar/gkw092	journal	February 2016
BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database Brůna, Tomáš; Hoff, Katharina J.; Lomsadze, Alexandre NAR Genomics and Bioinformatics, Vol. 3, Issue 1 https://doi.org/10.1093/nargab/lqaa108	journal	January 2021
Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training Ter-Hovhannisyan, V.; Lomsadze, A.; Chernoff, Y. O. Genome Research, Vol. 18, Issue 12 https://doi.org/10.1101/gr.081612.108	journal	October 2008
MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes Cantarel, B. L.; Korf, I.; Robb, S. M. C. Genome Research, Vol. 18, Issue 1 https://doi.org/10.1101/gr.6743907	journal	November 2007
Genome, transcriptome and methylome sequencing of a primitively eusocial wasp reveal a greatly reduced DNA methylation system in a social insect Standage, Daniel S.; Berens, Ali J.; Glastad, Karl M. Molecular Ecology, Vol. 25, Issue 8 https://doi.org/10.1111/mec.13578	journal	March 2016
Transposable elements and introgression introduce genetic variation in the invasive ant Cardiocondyla obscurior Errbii, Mohammed; Keilwagen, Jens; Hoff, Katharina J. Molecular Ecology, Vol. 30, Issue 23 https://doi.org/10.1111/mec.16099	journal	August 2021
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects Holt, Carson; Yandell, Mark BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-491	journal	December 2011
Gene finding in novel genomes Korf, Ian BMC Bioinformatics, Vol. 5, Issue 1 https://doi.org/10.1186/1471-2105-5-59	journal	May 2004
Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi Keilwagen, Jens; Hartung, Frank; Paulini, Michael BMC Bioinformatics, Vol. 19, Issue 1 https://doi.org/10.1186/s12859-018-2203-5	journal	May 2018
VARUS: sampling complementary RNA reads from the sequence read archive Stanke, Mario; Bruhn, Willy; Becker, Felix BMC Bioinformatics, Vol. 20, Issue 1 https://doi.org/10.1186/s12859-019-3182-x	journal	November 2019
TSEBRA: transcript selector for BRAKER Gabriel, Lars; Hoff, Katharina J.; Brůna, Tomáš BMC Bioinformatics, Vol. 22, Issue 1 https://doi.org/10.1186/s12859-021-04482-0	journal	November 2021
A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds Wallberg, Andreas; Bunikis, Ignas; Pettersson, Olga Vinnere BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-019-5642-0	journal	April 2019
High-Quality Assemblies for Three Invasive Social Wasps from the Vespula Genus Harrop, Thomas W. R.; Guhlin, Joseph; McLaughlin, Gemma M. G3 Genes\|Genomes\|Genetics, Vol. 10, Issue 10 https://doi.org/10.1534/g3.120.401579	journal	October 2020
Multifaceted quality assessment of gene repertoire annotation with OMArk Nevers, Yannis; Rossier, Victor; Train, Clément Zenodo https://doi.org/10.5281/zenodo.7359861	dataset	January 2022
Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi Keilwagen, Jens; Hartung, Frank; Paulini, Michael figshare https://doi.org/10.6084/m9.figshare.c.4116467.v1	collection	January 2018
A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds Wallberg, Andreas; Bunikis, Ignas; Pettersson, Olga Figshare https://doi.org/10.6084/m9.figshare.c.4463783.v1	collection	January 2019
VARUS: sampling complementary RNA reads from the sequence read archive Stanke, Mario; Bruhn, Willy; Becker, Felix figshare https://doi.org/10.6084/m9.figshare.c.4732031	collection	January 2019
Galba: genome annotation with miniprot and AUGUSTUS Brůna, Tomáš; Li, Heng; Guhlin, Joseph figshare https://doi.org/10.6084/m9.figshare.c.6815645.v1	collection	January 2023

Similar Records

BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA

Journal Article · 2024 · Genome Research · OSTI ID:2470762

Gabriel, Lars; Brůna, Tomáš; Hoff, Katharina J.; +4 more

Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community

Journal Article · 2017 · Database · OSTI ID:1625308

Saha, Surya; Hosmani, Prashant S.; Villalobos-Ayala, Krystal; +45 more

JGI Plant Genomics Gene Annotation Pipeline

Conference · 2014 · OSTI ID:1241222

Shu, Shengqiang; Rokhsar, Dan; Goodstein, David; +2 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
AUGUSTUS
Biochemistry & Molecular Biology
Biotechnology & Applied Microbiology
Gene prediction
Mathematical & Computational Biology
Miniprot
Protein coding gene

Title: Galba: genome annotation with miniprot and AUGUSTUS

Citation Formats

References (46)

Similar Records

Related Subjects