Using Tablet for visual exploration of second-generation sequencing data

You are here

TitleUsing Tablet for visual exploration of second-generation sequencing data
Publication TypeJournal Article
Year of Publication2013
AuthorsMilne, I, Stephen, G, Bayer, M, Cock, PJA, Pritchard, L, Cardle, L, Shaw, PD, Marshall, D
JournalBriefings in Bioinformatics
Volume14
Issue2
Pagination193 - 202
Date PublishedJan-03-2013
ISSN1467-5463
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 tablet@hutton.ac.uk.

URLhttp://bib.oxfordjournals.org/cgi/doi/10.1093/bib/bbs012
DOI10.1093/bib/bbs012
Short TitleBriefings in Bioinformatics
Refereed DesignationUnknown