NGV

Contents

  1. What is NGV?
  2. Screenshots

What is NGV?

With the increasing availability of High Throughput Sequencing (HTS) data, tools and methods for the analysis of these data become increasingly important. In their simplest form, such data sets consist of a (long) genomic sequence and a (large) set of short reads that were aligned/mapped with this sequence. Besides automatic processing it is sometimes desirable to manually analyze interesting regions in such data sets in order to judge on their quality as well as to derive conclusions regarding a particular experiment.

NGV pipeline

NGV is a data set preprocessor and a desktop application for the visual inspection of HTS data. In a preprocessing step, NGV takes a genomic sequence and a file containing mapped reads as input and creates several indices. This preprocessing step is easily extendable by a plug-in mechanism. Preprocessed data sets can then be loaded and visualized efficiently: NGV provides several information visualizations (coverage histogram, coverage overviews, detail view). It makes use of interval tree-based indices to efficiently visualize large HTS data sets and enable users to search for regions with a defined minimum coverage as well as for mismatches between consensus and reference sequence.

NGV screen shots

The following screenshot shows the NGV coverage visualizations (click the image for an enlarged version). The screenshot depicts an overview of a S. pombe ChIP-seq experiment. White pixels correspond to uncovered regions, dark red pixels to high-covered regions. Right-clicking a pixel-block displays a magnification. The background window shows a Hilbert-curve visualization, the foreground window a visualization where the sequence is drawn in a zig-zag pattern.

NGV genome overview

The following screenshot shows the NGV detail view (click the image for an enlarged version). The main canvas shows (from top to bottom) the currently chosen region of the reference sequence, a consensus and a coverage profile, the consensus (color-coded by coverage of the respective position) and the aligned reads. To the left, meta data of the currently selected data set are displayed.

NGV detail view