Evidence map›Paper›PMID 37090650›Full record

ArticlebioRxiv : the preprint server for biology2023

GALBA: Genome Annotation with Miniprot and AUGUSTUS.

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

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

10 authors.

Tomáš BrůnaUS Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA.
Heng LiDepartment of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA & Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
Joseph GuhlinGenomics Aotearoa and Laboratory for Evolution and Development, Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9016, New Zealand.
Daniel HonselInstitute of Computer Science, University of Göttingen, 37077 Göttingen, Germany.
Steffen HerboldFaculty for Computer Science and Mathematics, University of Passau, 94032 Passau, Germany.
Mario StankeInstitute of Mathematics and Computer Science & Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany.
Natalia NenashevaInstitute of Mathematics and Computer Science & Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany.
Matthis EbelInstitute of Mathematics and Computer Science & Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany.
Lars GabrielInstitute of Mathematics and Computer Science & Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany.
Katharina J HoffInstitute of Mathematics and Computer Science & Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany.

Funding

Advanced computational methods in analyzing high-throughput sequencing dataR01HG010040 · NHGRI · DANA-FARBER CANCER INST · PI Heng Li · 2018 to 2026
$3.7M
NIGMS Administrative Supplements to Support Undergraduate Summer ResearchR01GM128145 · NIGMS · GEORGIA INSTITUTE OF TECHNOLOGY · PI BORODOVSKY, MARK · 2018 to 2021
$1.1M
NHGRI NIH HHS R01 HG010040NIGMS NIH HHS R01 GM128145Wellcome Trust
6 · The paper itself

Abstract

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 previously unannotated 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.

Identifiers

PMID37090650
PMCPMC10120627

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.