SnoopCGH is a java desktop application for visualising and exploring comparative genomic hybridization (CGH) data. The software allows the user to interactively analyse several sets of data simultaneously. The input is based on a tab-, space- or comma-delimited format, containing series of log intensity values corresponding to one or more comparisons or samples.

SnoopCGH provides CGH plots with unlimited zoom (in both axes) that can be explored interactively with the mouse. The use of multiple layers, that can be stacked and combined, facilitates the visualization of the data. It is possible to apply several layers to a plot in order to filter the CGH ratios or perform statistical analysis in regions of interest. Analysis methods have been implemented and enable the rapid visualisation and dissection of putative structural variations (SVs).

In particular, data are smoothed using an algorithm based on Haar wavelets [1], and islands of potential SVs are estimated using SW-Array [2]. We remove outliers prior to estimation to increase robustness, and estimate levels of statistical significance and robustness of putative SVs using permutations. This quantification of putative SVs leads to an ability to rank the regions of interest. Other SV detection algorithms could be integrated in the future.

A powerful feature of SnoopCGH is its ability to interface with downloadable annotation files (e.g. embl) from genomic browsers, that include information on gene names and genomic features (e.g. GC content). The user has a visual representation of the annotations at the foot of the plot and can easily access detailed textual information by clicking on them or by textual searching. Direct links to the main genomic browsers are incorporated.

Download SnoopCGH
Download Express Manual (pdf)
Download Visual Introduction (pdf)
Watch Visual Introduction (flash presentation)

[1] Ben-Yaacov E, Eldar YC. A fast and flexible method for the segmentation of aCGH data. Bioinformatics 2008; 24:1139-45.
[2] Price TS et al. SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data. Nucleic Acids Res 2005; 33:3455-64.

Contact: jg10(at)