ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines.
ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines.
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DOI：
10.12688/f1000research.6157.2
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发表时间：
2015
期刊：
影响因子：
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通讯作者：
Amman F
中科院分区：
文献类型：
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作者：
Wolfinger MT;Fallmann J;Eggenhofer F;Amman F
下一代测序（NGS）技术的最新成就导致对可重用软件组件的高需求，以轻松编译用于大基因组学数据的定制分析工作流程。我们提出ViennaNGS，一个集成的Perl模块集合，专注于为NGS数据处理构建高效的管道。它具有从常见NGS文件格式提取和转换特征、计算和评估读段映射统计数据以及归一化RNA丰度的功能。此外，ViennaNGS还提供软件组件，用于从RNA-seq数据中识别和表征剪接点，解析和浓缩序列基序数据，自动构建UCSC基因组浏览器的Assembly和Track Hub，以及一组常用NGS命令行工具的包装程序。
Recent achievements in next-generation sequencing (NGS) technologies lead to a high demand for reuseable software components to easily compile customized analysis workflows for big genomics data. We present ViennaNGS, an integrated collection of Perl modules focused on building efficient pipelines for NGS data processing. It comes with functionality for extracting and converting features from common NGS file formats, computation and evaluation of read mapping statistics, as well as normalization of RNA abundance. Moreover, ViennaNGS provides software components for identification and characterization of splice junctions from RNA-seq data, parsing and condensing sequence motif data, automated construction of Assembly and Track Hubs for the UCSC genome browser, as well as wrapper routines for a set of commonly used NGS command line tools.