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Brief Bioinform. 2013 Mar;14(2):193-202. doi: 10.1093/bib/bbs012. Epub 2012 Mar 24.

Using Tablet for visual exploration of second-generation sequencing data.

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  • 1Information & Computational Sciences, The James Hutton Institute JHI, Dundee DD2 5DA, Scotland, UK. iain.milne@hutton.ac.uk

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.

PMID:
22445902
[PubMed - indexed for MEDLINE]
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