From GenPlay, Einstein Genome Analyzer
Rapidly decreasing sequencing cost due to the emergence and improvement of massively-parallel sequencing technologies has resulted in dramatic increase in the quantity of data that need to be analyzed. Therefore, software tools to process, visualize, analyze and integrate data produced on multiple platforms and using multiple methods are needed.
We will report on GenPlay, an extremely fast, easy to use and stable tool for rapid analysis and data processing that is being developed at Albert Einstein College of Medicine. Genplay, which is written in Java and runs on all major operating systems, can display data obtained either with micro-array based or sequencing based platforms. GenPlay displays tracks adapted to summarize gene structure, gene expression; repeat families, CPG islands, etc. GenPlay can also display custom tracks to show the results of RNA-seq, Chip-Seq or TimEX-seq analysis, for example.
GenPlay also offers a library of operations to process raw data (normalization, binning, smoothing) and to generate statistics (minimum, maximum, standard deviation, correlation etc). The tools provided include Gaussian filter, peak finders, signal saturation, island finders. It also has graphical features like scatter plots and bar charts to depict repartition and distances between genes.
The browser is currently being tested and used for in-house studies. The library of operations is growing based on the emerging needs. Contributions to the development of the software are welcome. The development team aims to release the first version of the software within this year.