Optimisation of SNP and Alternative Splicing Discovery using the Tablet NGS Viewer

The development of second and subsequent generation sequencing technologies introduces limitations on our ability to interrogate the results from analyses and identify patterns that reflect both major quality control issues, and biologically meaningful structures in datasets and complex data analysis outputs. In our crop and pathogen genetics work at the James Hutton Institute, we find that we are increasingly using visualization to support and aid in the understanding of these datasets.

Tablet has been designed as a high-performance application for the visualization of NGS sequence mapping and assemblies. We have found it to be of particular value in tuning and choosing appropriate parameters for the components of our analysis pipelines. In particular, we use Tablet for the identification of miss-mapping and miss-assembly errors which have significant implications for the generation of false positive SNPs or erroneous splice junctions. 

Tablet is written in Java with support for multiple desktop platforms (Windows, OSX and Linux) and is freely available in 32 and 64-bit formats from http://bioinf.hutton.ac.uk/tablet. Tablet was designed to handle large data sets, and has an easy installation routine with no complex software dependencies, along with support for a range of input formats and an intuitive, geneticist-friendly graphical interface. It has been widely deployed either directly on biologists’ desktops or as a component of integrated analysis pipelines.