TY - JOUR
T1 - Using tablet for visual exploration of second-generation sequencing data
AU - Milne, Iain
AU - Stephen, Gordon
AU - Bayer, Micha
AU - Cock, Peter J.A.
AU - Pritchard, Leighton
AU - Cardle, Linda
AU - Shawand, Paul D.
AU - Marshall, David
PY - 2013/3/31
Y1 - 2013/3/31
N2 - 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 [email protected].
AB - 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 [email protected].
KW - assembly validation
KW - second-generation sequencing
KW - visualization
UR - http://www.scopus.com/inward/record.url?scp=84875578097&partnerID=8YFLogxK
U2 - 10.1093/bib/bbs012
DO - 10.1093/bib/bbs012
M3 - Article
C2 - 22445902
AN - SCOPUS:84875578097
SN - 1467-5463
VL - 14
SP - 193
EP - 202
JO - Briefings in Bioinformatics
JF - Briefings in Bioinformatics
IS - 2
ER -