SolexaTools: An Open Source Sequence Analysis Framework Brian O’Connor Nelson Lab University of California, Los Angeles ht...
Illumina Data Flow <ul><li>We started with the basic data flow from the Illumina Genome Analyzer (images, sequence, qualit...
SolexaLIMS <ul><li>Java: Spring & Hibernate </li></ul><ul><li>Used to gather information about each sample needed for prop...
SolexaPipeline
SolexaPipeline
 
Alignment Reports BED & WIG files visualized in the UCSC Genome Browser
SolexaTools Release <ul><li>1.0 release this month: </li></ul><ul><ul><li>BLAT/ELAND/MAQ alignment algorithms </li></ul></...
Acknowledgements <ul><li>Jordan Mendler </li></ul><ul><li>Zugen Chen </li></ul><ul><li>Dmitriy Skvortsov </li></ul><ul><li...
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O Connor Solexa Tools Bosc2008

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O Connor Solexa Tools Bosc2008

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

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