Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, United States.
University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC 27710, United States.
Bioinformatics. 2023 Aug 1;39(8). doi: 10.1093/bioinformatics/btad516.
Many existing software libraries for genomics require researchers to pick between competing considerations: the performance of compiled languages and the accessibility of interpreted languages. Go, a modern compiled language, provides an opportunity to address this conflict. We introduce Gonomics, an open-source collection of command line programs and bioinformatic libraries implemented in Go that unites readability and performance for genomic analyses. Gonomics contains packages to read, write, and manipulate a wide array of file formats (e.g. FASTA, FASTQ, BED, BEDPE, SAM, BAM, and VCF), and can convert and interface between these formats. Furthermore, our modular library structure provides a flexible platform for researchers developing their own software tools to address specific questions. These commands can be combined and incorporated into complex pipelines to meet the growing need for high-performance bioinformatic resources.
Gonomics is implemented in the Go programming language. Source code, installation instructions, and documentation are freely available at https://github.com/vertgenlab/gonomics.
许多现有的基因组学软件库要求研究人员在竞争因素之间做出选择：编译语言的性能和解释语言的可访问性。Go 是一种现代的编译语言，为解决这一冲突提供了机会。我们引入了 Gonomics，这是一个用 Go 实现的开源命令行程序和生物信息学库集合，它为基因组分析统一了可读性和性能。Gonomics 包含用于读取、写入和操作各种文件格式（例如 FASTA、FASTQ、BED、BEDPE、SAM、BAM 和 VCF）的软件包，并可以在这些格式之间进行转换和接口。此外，我们的模块化库结构为开发人员提供了一个灵活的平台，用于开发自己的软件工具来解决特定问题。这些命令可以组合并纳入复杂的管道中，以满足对高性能生物信息学资源的不断增长的需求。
Gonomics 是用 Go 编程语言实现的。源代码、安装说明和文档可在 https://github.com/vertgenlab/gonomics 上免费获取。
