systemPipeR: NGS workflow and report generation environment.
systemPipeR: NGS workflow and report generation environment.
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DOI：
10.1186/s12859-016-1241-0
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发表时间：
2016-09-20
影响因子：
3
通讯作者：
Girke T
中科院分区：
文献类型：
--
作者：
H Backman TW;Girke T
下一代测序（NGS）彻底改变了生物学和医学许多领域的研究方式。然而，对NGS数据的分析仍然是有效利用该技术的主要障碍，因为它需要对大数据进行复杂的多步处理，需要用户提供大量的计算专业知识。虽然已经投入了大量的精力开发专用于NGS实验的各个分析步骤的软件，但目前没有足够的资源将广泛使用的R/Bioconductor环境中的各个软件组件集成到自动化工作流程中，该自动化工作流程能够以时间有效和可重复的方式从头到尾运行大多数类型的NGS应用程序的分析。为了满足这一需求，我们开发了R/Bioconductor封装系统PipeR。它是一个可扩展的环境，用于构建和运行端到端分析工作流，并为各种NGS应用程序自动生成报告。它的独特功能包括跨不同NGS应用程序的统一工作流界面，自动生成报告，以及支持在本地计算机和计算机集群上运行R和命令行软件。灵活的样品注释基础设施可有效处理复杂的样品集和实验设计。为了简化广泛使用的NGS应用程序的分析，该软件包为RNA-Seq，ChIP-Seq，VAR-Seq和Ribo-Seq提供了预配置的工作流程和报告模板。今后将提供更多的工作流程模板。systemPipeR加速了从NGS实验中提取可重现的分析结果。通过结合许多R/Bioconductor和命令行工具的功能，它可以有效地利用现有的软件资源，而不会限制用户使用一组预定义的方法或环境。systemPipeR可从Bioconductor（http：//bioconductor.org/packages/devel/systemPipeR）免费获得用于所有常见操作系统。本文的在线版本（doi：10.1186/s12859-016-1241-0）包含补充材料，可供授权用户使用。
Next-generation sequencing (NGS) has revolutionized how research is carried out in many areas of biology and medicine. However, the analysis of NGS data remains a major obstacle to the efficient utilization of the technology, as it requires complex multi-step processing of big data demanding considerable computational expertise from users. While substantial effort has been invested on the development of software dedicated to the individual analysis steps of NGS experiments, insufficient resources are currently available for integrating the individual software components within the widely used R/Bioconductor environment into automated workflows capable of running the analysis of most types of NGS applications from start-to-finish in a time-efficient and reproducible manner. To address this need, we have developed the R/Bioconductor package systemPipeR. It is an extensible environment for both building and running end-to-end analysis workflows with automated report generation for a wide range of NGS applications. Its unique features include a uniform workflow interface across different NGS applications, automated report generation, and support for running both R and command-line software on local computers and computer clusters. A flexible sample annotation infrastructure efficiently handles complex sample sets and experimental designs. To simplify the analysis of widely used NGS applications, the package provides pre-configured workflows and reporting templates for RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. Additional workflow templates will be provided in the future. systemPipeR accelerates the extraction of reproducible analysis results from NGS experiments. By combining the capabilities of many R/Bioconductor and command-line tools, it makes efficient use of existing software resources without limiting the user to a set of predefined methods or environments. systemPipeR is freely available for all common operating systems from Bioconductor (http://bioconductor.org/packages/devel/systemPipeR). The online version of this article (doi:10.1186/s12859-016-1241-0) contains supplementary material, which is available to authorized users.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
48
作者：
Huber W;Carey VJ;Gentleman R;Anders S;Carlson M;Carvalho BS;Bravo HC;Davis S;Gatto L;Girke T;Gottardo R;Hahne F;Hansen KD;Irizarry RA;Lawrence M;Love MI;MacDonald J;Obenchain V;Oleś AK;Pagès H;Reyes A;Shannon P;Smyth GK;Tenenbaum D;Waldron L;Morgan M
通讯作者：
Morgan M
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
5.8
作者：
Goodstadt, Leo
通讯作者：
Goodstadt, Leo
影响因子：
12.3
作者：
Akalin A;Kormaksson M;Li S;Garrett-Bakelman FE;Figueroa ME;Melnick A;Mason CE
通讯作者：
Mason CE