SePIA: RNA and small RNA sequence processing, integration, and analysis.
SePIA: RNA and small RNA sequence processing, integration, and analysis.
复制标题
DOI：
10.1186/s13040-016-0099-z
复制
发表时间：
2016
期刊：
影响因子：
4.5
通讯作者：
Hautaniemi S
中科院分区：
文献类型：
--
作者：
Icay K;Chen P;Cervera A;Rantanen V;Lehtonen R;Hautaniemi S
大规模的测序实验是复杂的，需要广泛的计算工具来提取和解释相关的生物信息。在需要对小RNA和互补RNA数据进行单独处理和综合分析的项目中尤其如此。这类研究将受益于易于实施的计算工作流程，并使两种排序数据类型的处理和分析标准化。我们开发了SECEIA(序列处理、集成和分析)，这是一个全面的小RNA和RNA工作流程。它在已建立的工作流引擎之上为20多个常见的RNA-seq工具提供了现成的执行，并提供了动态流水线体系结构来管理、单独分析和集成小RNA和RNA数据。通过Docker的实施，使Sepia可移植并易于运行。我们通过两个涉及三个乳腺癌数据集的案例研究来展示该工作流程的广泛实用性。Sepia可以直接配置结果，并将结果组织成可阅读的HTML报告。此外，底层流水线引擎支持计算资源管理以实现最佳性能。Sepia是一个开放源码的工作流程，引入了对RNA和小RNA数据的标准化处理和分析。Sepia的模块化设计使您能够针对给定的实验进行强大的定制，同时保持整体的工作流程结构。它在http://anduril.org/sepia.上有售本文的在线版本(doi：10.1186/s13040-0160099-z)包含补充材料，授权用户可以使用。
Large-scale sequencing experiments are complex and require a wide spectrum of computational tools to extract and interpret relevant biological information. This is especially true in projects where individual processing and integrated analysis of both small RNA and complementary RNA data is needed. Such studies would benefit from a computational workflow that is easy to implement and standardizes the processing and analysis of both sequenced data types. We developed SePIA (Sequence Processing, Integration, and Analysis), a comprehensive small RNA and RNA workflow. It provides ready execution for over 20 commonly known RNA-seq tools on top of an established workflow engine and provides dynamic pipeline architecture to manage, individually analyze, and integrate both small RNA and RNA data. Implementation with Docker makes SePIA portable and easy to run. We demonstrate the workflow’s extensive utility with two case studies involving three breast cancer datasets. SePIA is straightforward to configure and organizes results into a perusable HTML report. Furthermore, the underlying pipeline engine supports computational resource management for optimal performance. SePIA is an open-source workflow introducing standardized processing and analysis of RNA and small RNA data. SePIA’s modular design enables robust customization to a given experiment while maintaining overall workflow structure. It is available at http://anduril.org/sepia. The online version of this article (doi:10.1186/s13040-016-0099-z) contains supplementary material, which is available to authorized users.