ASAP: an environment for automated preprocessing of sequencing data.
ASAP: an environment for automated preprocessing of sequencing data.
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DOI：
10.1186/1756-0500-6-5
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发表时间：
2013-01-04
影响因子：
1.8
通讯作者：
Li C
中科院分区：
文献类型：
--
作者：
Torstenson ES;Li B;Li C
下一代测序（NGS）为遗传学研究提供了前所未有的大量数据。处理从原始序列读取到变量调用的数据是一项艰巨的任务，手动处理这些数据可能会大大延迟下游分析，并增加人为错误的可能性。研究界已经开发了一些工具来正确地准备序列数据进行分析，并建立了指导方针，指导如何应用这些工具来实现最佳结果，然而，现有的管道程序将整个过程自动化，要么是研究人员无法访问的，要么是基于网络的，需要一定的管理专业知识来设置。开发高级序列自动化管道（ASAP）是为了提供一个框架，用于将测序数据自动转换为带注释的变体调用，其目标是在不需要专用硬件或管理权限的情况下最大限度地减少用户的参与。ASAP既可以在计算机集群上工作，也可以在独立的机器上工作，人工参与最少，并保持高度的数据完整性，同时允许完全控制其组件程序的配置。它提供了一个易于使用的界面，用于提交和跟踪作业以及恢复失败的作业。它还提供了用于质量检查和将作业分成多个部分以获得最大吞吐量的工具。ASAP为NGS数据预处理提供了一个构建自动化流水线的环境。这种环境对于使用和未来的开发是灵活的。它可以在http://biostat.mc.vanderbilt.edu/ASAP上免费获得。
Next-generation sequencing (NGS) has yielded an unprecedented amount of data for genetics research. It is a daunting task to process the data from raw sequence reads to variant calls and manually processing this data can significantly delay downstream analysis and increase the possibility for human error. The research community has produced tools to properly prepare sequence data for analysis and established guidelines on how to apply those tools to achieve the best results, however, existing pipeline programs to automate the process through its entirety are either inaccessible to investigators, or web-based and require a certain amount of administrative expertise to set up. Advanced Sequence Automated Pipeline (ASAP) was developed to provide a framework for automating the translation of sequencing data into annotated variant calls with the goal of minimizing user involvement without the need for dedicated hardware or administrative rights. ASAP works both on computer clusters and on standalone machines with minimal human involvement and maintains high data integrity, while allowing complete control over the configuration of its component programs. It offers an easy-to-use interface for submitting and tracking jobs as well as resuming failed jobs. It also provides tools for quality checking and for dividing jobs into pieces for maximum throughput. ASAP provides an environment for building an automated pipeline for NGS data preprocessing. This environment is flexible for use and future development. It is freely available at http://biostat.mc.vanderbilt.edu/ASAP.