Using Tablet for visual exploration of second-generation sequencing data

Iain Milne, Gordon Stephen, Micha Bayer, Peter J A Cock, Leighton Pritchard, Linda Cardle, Paul D Shaw, David Marshall

Research output: Contribution to journalArticle

455 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)193-202
Number of pages10
JournalBriefings in Bioinformatics
Volume14
Issue number2
DOIs
Publication statusPrint publication - Mar 2013
Externally publishedYes

Keywords

  • Animals
  • Computational Biology
  • Computer Graphics
  • Data Display
  • Databases, Genetic/statistics & numerical data
  • Genomics/statistics & numerical data
  • High-Throughput Nucleotide Sequencing/statistics & numerical data
  • Humans
  • Internet
  • Sequence Analysis/statistics & numerical data
  • Software

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  • Cite this

    Milne, I., Stephen, G., Bayer, M., Cock, P. J. A., Pritchard, L., Cardle, L., Shaw, P. D., & Marshall, D. (2013). Using Tablet for visual exploration of second-generation sequencing data. Briefings in Bioinformatics, 14(2), 193-202. https://doi.org/10.1093/bib/bbs012