Using Tablet for visual exploration of second-generation sequencing data

TLDR

Second‑generation sequencing generates large volumes of short reads in diverse formats, posing significant visualization challenges. This article demonstrates how Tablet, a high‑performance graphical viewer, facilitates analysis of 2GS assemblies and read mappings. Tablet employs efficient computing and visualization techniques to deliver a responsive interface that supports multiple file formats and features such as whole‑reference coverage overviews, variant highlighting, paired‑end read markup, GFF3‑based feature tracks, and protein translations. Tablet installers are freely available for 32‑ or 64‑bit Windows, OS X, Linux, and Solaris at http://bioinf.hutton.ac.uk/tablet. For further details, contact [e-mail].

Abstract

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 from http://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 [e-mail].