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- Title
GenPlay, a multipurpose genome analyzer and browser.
- Authors
Lajugie, Julien; Bouhassira, Eric E.
- Abstract
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 microarray- or sequencing-based platforms and offers a library of operations (normalization, binning, smoothing) to process raw data into visualizable 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 single nucleotide polymorphism (SNP) analysis. GenPlay can generate statistics (minimum, maximum, SD, 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.eduSupplementary information: Supplementary data are available at Bioinformatics online.
- Subjects
BIOINFORMATICS software; GENOMIC information retrieval; PARALLEL processing; DATA analysis; ELECTRONIC data processing; COMPUTER operating systems; JAVA programming language; GENE expression
- Publication
Bioinformatics, 2011, Vol 27, Issue 14, p1889
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btr309