Using Tablet for visual exploration of second-generation sequencing data
Using Tablet for visual exploration of second-generation sequencing data
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DOI：
10.1093/bib/bbs012
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发表时间：
2013-03-01
影响因子：
9.5
通讯作者：
Marshall, David
中科院分区：
文献类型：
--
作者：
Milne, Iain;Stephen, Gordon;Marshall, David
第二代测序技术（2GS）的出现为序列集的可视化提供了一系列重大的新挑战。这些问题包括正在产生的大量数据、短读长度以及与新测序技术的多样性有关的不同数据类型和数据格式。本文说明了tablet（用于可视化2GS组件和读取映射的高性能图形查看器）如何在分析这些数据中发挥重要作用。我们展示了Tablet，并通过一系列用例，展示了它在质量保证和科学发现方面的价值，通过全参考覆盖概述、变体突出显示、成对端读取标记、基于gff3的特征轨迹和蛋白质翻译等功能。我们讨论了用于提供丰富的响应性图形环境的计算和可视化技术，使用户能够轻松地查看一系列文件格式。平板电脑安装程序可以从http://bioinf.hutt.ac免费下载。32或64位版本，适用于Windows， OS X， Linux或Solaris。欲了解更多有关平板电脑的详细信息，请联系tablet@hutton.ac.uk。
The advent of second-generation sequencing (2GS) has provided a range of significant new challenges for the visualization of sequence assemblies. These include the large volume of data being generated, short-read lengths and different data types and data formats associated with the diversity of new sequencing technologies. This article illustrates how Tablet-a high-performance graphical viewer for visualization of 2GS assemblies and read mappings-plays an important role in the analysis of these data. We present Tablet, and through a selection of use cases, demonstrate its value in quality assurance and scientific discovery, through features such as whole-reference coverage overviews, variant highlighting, paired-end read mark-up, GFF3-based feature tracks and protein translations. We discuss the computing and visualization techniques utilized to provide a rich and responsive graphical environment that enables users to view a range of file formats with ease. Tablet installers can be freely downloaded frohttp://bioinf.hutton.ac.uk/tablet in 32 or 64-bit versions for Windows, OS X, Linux or Solaris. For further details on the Tablet, contact tablet@hutton.ac.uk.