GenPlay, a multipurpose genome analyzer and browser

Julien Lajugie, Eric E. Bouhassira

Research output: Contribution to journalArticle

16 Citations (Scopus)

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 sequencingbased 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.

Original languageEnglish (US)
Article numberbtr309
Pages (from-to)1889-1893
Number of pages5
JournalBioinformatics
Volume27
Issue number14
DOIs
StatePublished - Jul 2011

Fingerprint

Genome
Genes
Islands
Libraries
Software
Microarrays
Nucleotides
Polymorphism
RNA
Gene expression
Sequencing
High-Throughput Nucleotide Sequencing
Display devices
Statistics
Bar chart
Scatter diagram
Gaussian Filter
Binning
Single Nucleotide Polymorphism
Single nucleotide Polymorphism

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

GenPlay, a multipurpose genome analyzer and browser. / Lajugie, Julien; Bouhassira, Eric E.

In: Bioinformatics, Vol. 27, No. 14, btr309, 07.2011, p. 1889-1893.

Research output: Contribution to journalArticle

Lajugie, Julien ; Bouhassira, Eric E. / GenPlay, a multipurpose genome analyzer and browser. In: Bioinformatics. 2011 ; Vol. 27, No. 14. pp. 1889-1893.
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