The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data
The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data
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DOI：
10.1186/s12864-016-3288-8
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发表时间：
2016-11-18
期刊：
影响因子：
4.4
通讯作者：
Bucher, Philipp
中科院分区：
文献类型：
--
作者：
Ambrosini, Giovanna;Dreos, Rene;Bucher, Philipp
背景：ChIP-seq和相关的高通量染色质分析检测产生了越来越多的高价值生物学数据。为了理解它，生物学家需要通用的，高效的和用户友好的工具来访问，可视化和迭代分析这样的data.Results：在这里，我们提出了ChIP-Seq命令行工具和Web服务器，实现基本算法的ChIP-Seq数据分析开始与读取对齐文件。这些工具针对内存效率和速度进行了优化，从而允许在廉价的硬件上处理大量数据。网络界面提供了对大型公共数据库的访问。ChIP-Seq工具具有模块化和可互操作的设计，其中一个应用程序的输出可以作为另一个应用程序的输入。复杂和创新的任务，因此可以通过运行几个工具cascades.Conclusions：各种ChIP-Seq命令行工具和网络服务的计算效率，方便访问公共数据和互操作性方面的相关生物信息学资源的补充或媲美其他基于网络的工具。
Background: ChIP-seq and related high-throughput chromatin profilig assays generate ever increasing volumes of highly valuable biological data. To make sense out of it, biologists need versatile, efficient and user-friendly tools for access, visualization and itegrative analysis of such data.Results: Here we present the ChIP-Seq command line tools and web server, implementing basic algorithms for ChIP-seq data analysis starting with a read alignment file. The tools are optimized for memory-efficiency and speed thus allowing for processing of large data volumes on inexpensive hardware. The web interface provides access to a large database of public data. The ChIP-Seq tools have a modular and interoperable design in that the output from one application can serve as input to another one. Complex and innovative tasks can thus be achieved by running several tools in a cascade.Conclusions: The various ChIP-Seq command line tools and web services either complement or compare favorably to related bioinformatics resources in terms of computational efficiency, ease of access to public data and interoperability with other web-based tools.