U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Department of Data Sciences, Dana-Farber Cancer Institute, Boston, 02215, MA, USA.
BMC Bioinformatics. 2023 Aug 31;24(1):327. doi: 10.1186/s12859-023-05449-z.
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.
地球生物基因组计划迅速增加了可用的真核生物基因组数量，但大多数发布的基因组仍然缺乏对蛋白质编码基因的注释。此外，一些基因组还没有转录组数据。
已经开发了各种基因注释工具，但每种工具都有其局限性。在这里，我们介绍了 GALBA，这是一个完全自动化的流水线，利用快速蛋白质到基因组比对器 miniprot 与 AUGUSTUS 相结合，以高精度预测基因。准确性结果表明，GALBA 在注释大型脊椎动物基因组方面特别强大。我们还介绍了昆虫、脊椎动物和陆地植物的应用案例。GALBA 是完全开源的，并作为一个 Docker 镜像提供，以便在高性能计算环境中使用 Singularity 轻松执行。
我们的流水线解决了新测序基因组中准确基因注释的关键需求，我们相信 GALBA 将极大地促进不同生物的基因组注释。
