Sunday, May 22, 2011

GenPlay, a multi-purpose genome analyzer and browser

GenPlay, a multi-purpose genome analyzer and browser:

Motivation: Rapidly decreasing sequencing cost due to the emergence and improvement of massively-parallel sequencing technologies has resulted in a dramatic increase in the quantity of data that needs to be analyzed. Therefore, software tools to process, visualize, analyze and integrate data produced on multiple platforms and using multiple methods are needed.

Results: GenPlay is a fast, easy to use and stable tool for rapid analysis and data processing. It is written in Java and runs on all major operating systems. GenPlay recognizes a wide variety of common genomic data formats from micro-array or sequencing based platforms and offers a library of operations (normalization, binning, smoothing) to process raw data into visualisable tracks. GenPlay displays tracks adapted to summarize gene structure, gene expression, repeat families, CPG islands, etc. as well as custom tracks to show the results of RNA-Seq, ChIP-Seq, TimEX-Seq and SNP analysis. GenPlay can generate statistics (minimum, maximum, standard deviation, correlation, etc). The tools provided include Gaussian filter, peak finders, signal saturation, island finders. The software also offers graphical features such as scatter plots and bar charts to depict signal repartition. The library of operations is continuously growing based on the emerging needs.

Availability: GenPlay is an open source project available from http://www.genplay.net. The code source of the software is available at https://genplay.einstein.yu.edu/svn/GenPlay

Contact:eric.bouhassira@einstein.yu.edu


(Via Bioinformatics - Advance Access.)