O Connor Solexa Tools Bosc2008

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  • 1. SolexaTools: An Open Source Sequence Analysis Framework Brian O’Connor Nelson Lab University of California, Los Angeles http://solexatools.sourceforge.net
  • 2. Illumina Data Flow
    • We started with the basic data flow from the Illumina Genome Analyzer (images, sequence, quality score)‏
    • Several components needed to be written
      • LIMS
      • Alignment Plugins
      • Reporting Tools
  • 3. SolexaLIMS
    • Java: Spring & Hibernate
    • Used to gather information about each sample needed for proper analysis
    • Easy to use
  • 4. SolexaPipeline
  • 5. SolexaPipeline
  • 6.  
  • 7. Alignment Reports BED & WIG files visualized in the UCSC Genome Browser
  • 8. SolexaTools Release
    • 1.0 release this month:
      • BLAT/ELAND/MAQ alignment algorithms
      • genomic/cDNA/digital gene expression/targeted sequencing/tagged sequences
      • LIMS supporting external/internal users
    • 2.0 release:
      • Support other sequencers (e.g. SOLiD)‏
      • Name change
      • Support other experimental methods
      • Better pipelining environment
  • 9. Acknowledgements
    • Jordan Mendler
    • Zugen Chen
    • Dmitriy Skvortsov
    • Nils Homer
    • Barry Merriman
    • Stan Nelson
    http://solexatools.sourceforge.net