Brettin Thomas, Davis James J, Disz Terry, Edwards Robert A, Gerdes Svetlana, Olsen Gary J, Olson Robert, Overbeek Ross, Parrello Bruce, Pusch Gordon D, Shukla Maulik, Thomason James A, Stevens Rick, Vonstein Veronika, Wattam Alice R, Xia Fangfang
1] Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne IL, 60439, USA [2] Computation Institute, University of Chicago, Chicago, Illinois, 60637, USA.
Fellowship for Interpretation of Genomes, Burr Ridge, IL, 60527, USA.
Sci Rep. 2015 Feb 10;5:8365. doi: 10.1038/srep08365.
The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.
RAST（利用子系统技术进行快速注释）注释引擎于2008年构建，用于注释细菌和古菌基因组。它通过提供一个标准的软件管道来识别基因组特征（即蛋白质编码基因和RNA）并注释其功能。最近，为了使RAST成为更有用的研究工具并跟上生物信息学的发展，构建一个可定制且可扩展的RAST版本变得很有必要。在本文中，我们描述了RAST工具包（RASTtk），这是RAST的模块化版本，使研究人员能够构建自定义注释管道。RASTtk提供了用于识别和注释基因组特征的软件选择，以及向注释任务添加自定义特征的能力。RASTtk还支持基因组的批量提交以及为批量提交自定义注释协议的能力。这是RAST自成立以来的首次重大软件结构调整。
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