Center for Public Health Genomics, University of Virginia, PO Box 800717, Charlottesville, VA, 22908, USA.
Department of Biochemistry and Molecular Genetics, University of Virginia, PO Box 800733, Charlottesville, VA, 22908, USA.
Gigascience. 2020 Feb 1;9(2). doi: 10.1093/gigascience/giz149.
Reference genome assemblies are essential for high-throughput sequencing analysis projects. Typically, genome assemblies are stored on disk alongside related resources; e.g., many sequence aligners require the assembly to be indexed. The resulting indexes are broadly applicable for downstream analysis, so it makes sense to share them. However, there is no simple tool to do this.
Here, we introduce refgenie, a reference genome assembly asset manager. Refgenie makes it easier to organize, retrieve, and share genome analysis resources. In addition to genome indexes, refgenie can manage any files related to reference genomes, including sequences and annotation files. Refgenie includes a command line interface and a server application that provides a RESTful API, so it is useful for both tool development and analysis.
Refgenie streamlines sharing genome analysis resources among groups and across computing environments. Refgenie is available at https://refgenie.databio.org.
参考基因组组装对于高通量测序分析项目至关重要。通常，基因组组装与相关资源一起存储在磁盘上；例如，许多序列比对器需要对组装进行索引。生成的索引广泛适用于下游分析，因此共享它们是有意义的。但是，没有简单的工具可以做到这一点。
在这里，我们介绍了 refgenie，这是一个参考基因组组装资产管理工具。Refgenie 使组织、检索和共享基因组分析资源变得更加容易。除了基因组索引外，refgenie 还可以管理任何与参考基因组相关的文件，包括序列和注释文件。Refgenie 包括一个命令行接口和一个服务器应用程序，提供了一个 RESTful API，因此它对于工具开发和分析都非常有用。
Refgenie 简化了在小组之间以及跨计算环境共享基因组分析资源的流程。Refgenie 可在 https://refgenie.databio.org 上获取。
