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. Shawand, David Marshall

Research output: Contribution to journalArticle

392 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 Tabletça high-performance graphical viewer for visualization of 2GS assemblies and read mappingsçplays 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 theTablet, contact tablet@hutton.ac.uk.

LanguageEnglish
Pages193-202
Number of pages10
JournalBriefings in Bioinformatics
Volume14
Issue number2
DOIs
Publication statusPublished - 31 Mar 2013

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Tablets
Visualization
Quality assurance
Protein Biosynthesis
Proteins
Technology
Linux

Keywords

  • assembly validation
  • second-generation sequencing
  • visualization

Cite this

Milne, I., Stephen, G., Bayer, M., Cock, P. J. A., Pritchard, L., Cardle, L., ... 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
Milne, Iain ; Stephen, Gordon ; Bayer, Micha ; Cock, Peter J.A. ; Pritchard, Leighton ; Cardle, Linda ; Shawand, Paul D. ; Marshall, David. / Using tablet for visual exploration of second-generation sequencing data. In: Briefings in Bioinformatics. 2013 ; Vol. 14, No. 2. pp. 193-202.
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Milne, I, Stephen, G, Bayer, M, Cock, PJA, Pritchard, L, Cardle, L, Shawand, PD & Marshall, D 2013, 'Using tablet for visual exploration of second-generation sequencing data' Briefings in Bioinformatics, vol. 14, no. 2, pp. 193-202. https://doi.org/10.1093/bib/bbs012

Using tablet for visual exploration of second-generation sequencing data. / Milne, Iain; Stephen, Gordon; Bayer, Micha; Cock, Peter J.A.; Pritchard, Leighton; Cardle, Linda; Shawand, Paul D.; Marshall, David.

In: Briefings in Bioinformatics, Vol. 14, No. 2, 31.03.2013, p. 193-202.

Research output: Contribution to journalArticle

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