CLC bio<br />A Comprehensive Platform<br />for NGS Data Analysis<br />Saul A. Kravitz, PhD<br />Director of Consulting Ser...
Before the Flood<br />2005:   $5M Human genome – 19 sequencer years <br />Sample Prep<br />Analysis<br />Sequencing<br />S...
Nextgen Sequencing Revolution<br />2010:   $6k Human genome ~1 sequencer day<br />Help!!<br />Sample Prep<br />Analysis<br...
Bioinformatics Challenges<br /><ul><li>Data Analysis Tools for Biomedical Researchers
GUI-driven
HPC integration
Unprecedented data volumes
Rapid technology change, applications growth
Multi-platform data integration
No one-size-fits-all solutions
Rapid customization and adaptation</li></li></ul><li>CLC bio NGS Analysis Platform<br />CLC Genomics Workbench<br />CLC Ge...
Swiss Army Knife of NGS Analysis<br />SDK<br />Intuitive GUI<br />Traditional <br />Bioinformatics<br />Visualization<br /...
Why not use free tools?<br />Are tools free or “free”?<br />Tools vs solutions<br />True cost of ownership<br />Ease of Us...
Small RNA Analysis(in Beta soon)<br />Identify and filter/trim adapters <br />annotate using mirBASE and other resources<b...
De Novo Assembler<br />Human assembly of  38x Illumina paired-end<br />CLC Quality equivalent to Abyss<br />CLC:      7 hr...
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CLC bio presentation at 5th SFAF 6/3/2010

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My presentation at the 5th Sequencing FInishing and Analysis in the Future (SFAF -- http://www.lanl.gov/conferences/finishfuture/2010SFAF_Meeting_Guide.pdf) June 3, 2010

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  • GUI-driven tools and workflows
  • - miRNA workflow leveraging mirBASE and other resources
  • Very fast, small memory footprint
  •    SISPA = Sequence Independent Single Primer Amplification (if that needs spelling out) – amplifies and barcodes DNA moleculesAlso, if people are interested, can also mention availability of Danny Katzel’s cas2consed software.
  • CustomizationJava plug-in architecture for Server and WorkbenchOptimized “Cell” command line tools for efficient HPCWizard-based integration of customer toolsServer integration via SOAP and Command Line*
  • CLC bio presentation at 5th SFAF 6/3/2010

    1. 1. CLC bio<br />A Comprehensive Platform<br />for NGS Data Analysis<br />Saul A. Kravitz, PhD<br />Director of Consulting Services<br />
    2. 2. Before the Flood<br />2005: $5M Human genome – 19 sequencer years <br />Sample Prep<br />Analysis<br />Sequencing<br />Science<br />
    3. 3. Nextgen Sequencing Revolution<br />2010: $6k Human genome ~1 sequencer day<br />Help!!<br />Sample Prep<br />Analysis<br />Sequencing<br />Science<br />
    4. 4. Bioinformatics Challenges<br /><ul><li>Data Analysis Tools for Biomedical Researchers
    5. 5. GUI-driven
    6. 6. HPC integration
    7. 7. Unprecedented data volumes
    8. 8. Rapid technology change, applications growth
    9. 9. Multi-platform data integration
    10. 10. No one-size-fits-all solutions
    11. 11. Rapid customization and adaptation</li></li></ul><li>CLC bio NGS Analysis Platform<br />CLC Genomics Workbench<br />CLC Genomics Server<br /> CLC Assembly Cell<br />Developer SDK<br />Easy to use, Wizard-driven Desktop Software<br />Enterprise solution<br />High performance NGS algorithms<br />Workbench and Server Customization<br />
    12. 12. Swiss Army Knife of NGS Analysis<br />SDK<br />Intuitive GUI<br />Traditional <br />Bioinformatics<br />Visualization<br />Desktop Solutions<br />EnterpriseSolutions<br />High Performance<br />File Format Conversion<br />Tools Integration<br />Epigenomics<br />Transcriptomics<br />Genomics<br />RNA-Seq<br />miRNA<br />Read Mapping<br />De Novo Assembly<br />SNP/DIP Detection<br />CHIP-Seq<br />
    13. 13. Why not use free tools?<br />Are tools free or “free”?<br />Tools vs solutions<br />True cost of ownership<br />Ease of Use<br />Tools integration<br />Support<br />
    14. 14. Small RNA Analysis(in Beta soon)<br />Identify and filter/trim adapters <br />annotate using mirBASE and other resources<br />- target species of interest <br />Merge/group by mature, precursor/reference <br />Fully integrated with expression analysis<br />
    15. 15. De Novo Assembler<br />Human assembly of 38x Illumina paired-end<br />CLC Quality equivalent to Abyss<br />CLC: 7 hrs, 1 node, 42 Gbof RAM<br />Abyss: 80 hrs, 21 nodes, 336 Gbof RAM<br />Metagenomics Assembly<br />METAHIT Dataset MH0041 40M 75bp paired end<br />3 hrs on desktop, 6 Gb RAM<br />Higher N50 and Total Contig Size than Reported<br />
    16. 16. Viral Sequencing at JCVI(See Nadia Fedorova’s Poster!)<br />Amplify and Barcode using SISPA, 454 + Illumina Sequencing<br />Depth of coverage sometimes >1000x<br />De novo Assembly of Consensus for all Segments<br />For each segment:<br />Map reads from each technology independently using best full length reference from NCBI, call variations<br />Update reference with variations confirmed by multiple technologies<br />Map reads using updated reference and all reads<br />Convert to consed, analyze, order Sanger closure reactions<br />Source: Jessica Hostetler, Nadia Federova, Tim Stockwell, Danny Katzel<br />
    17. 17. Why CLC bioTools?<br />CLC handled hybrid sequencing technologies directly <br />Very biased coverage confounded other assemblers that expect random arrival stats.  CLC didn’t seem to suffer from biased coverage.  <br />Very accurate SNP calls in areas of deep coverage.<br /> Tim Stockwell Director of Viral Informatics J. Craig Venter Institute<br />
    18. 18. Targeted Resequencing QC<br />Assessment of targeted sequencing technology<br />Coverage Statistics for Targeted Regions<br />Very short schedule, limited bioinformatics staff<br />Plug-in development leveraging CLC tools to automate the process and meet short deadline<br />QC Report now available as plug-in<br />
    19. 19. Professional Services<br />Developing customized solutions<br />Integration with LIMS, workflows, DB<br />Bioinformatics Algorithm Development<br />Cloud and Grid Integration<br />Data Analysis<br />
    20. 20. Questions?<br />Saul A. Kravitz, PhD<br />skravitz@clcbio.com<br />(301)355-0813<br />Thank you for listening<br />
    21. 21. Questions<br />Saul A. Kravitz, PhD<br />skravitz @ clcbio.com <br />301)355-0813<br />Thank you for listening<br />

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