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CLC bio A Comprehensive Platform for NGS Data Analysis Saul A. Kravitz, PhD Director of Consulting Services
Before the Flood 2005:   $5M Human genome – 19 sequencer years  Sample Prep Analysis Sequencing Science
Nextgen Sequencing Revolution 2010:   $6k Human genome ~1 sequencer day Help!! Sample Prep Analysis Sequencing Science
Bioinformatics Challenges ,[object Object]
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,[object Object]
Swiss Army Knife of NGS Analysis SDK Intuitive GUI Traditional  Bioinformatics Visualization Desktop Solutions EnterpriseSolutions High Performance File Format Conversion Tools Integration Epigenomics Transcriptomics Genomics RNA-Seq miRNA Read Mapping De Novo Assembly SNP/DIP Detection CHIP-Seq
Why not use free tools? Are tools free or “free”? Tools vs solutions True cost of ownership Ease of Use Tools integration Support
Small RNA Analysis(in Beta soon) Identify and filter/trim adapters  annotate using mirBASE and other resources - target species of interest  Merge/group by mature, precursor/reference  Fully integrated with expression analysis
De Novo Assembler Human assembly of  38x Illumina paired-end CLC Quality equivalent to Abyss CLC:      7 hrs, 1 node,       42 Gbof RAM Abyss:  80 hrs, 21 nodes, 336 Gbof RAM Metagenomics Assembly METAHIT Dataset MH0041 40M 75bp paired end 3 hrs on desktop, 6 Gb RAM Higher N50 and Total Contig Size than Reported

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CLC bio presentation at 5th SFAF 6/3/2010

  • 1. CLC bio A Comprehensive Platform for NGS Data Analysis Saul A. Kravitz, PhD Director of Consulting Services
  • 2. Before the Flood 2005: $5M Human genome – 19 sequencer years Sample Prep Analysis Sequencing Science
  • 3. Nextgen Sequencing Revolution 2010: $6k Human genome ~1 sequencer day Help!! Sample Prep Analysis Sequencing Science
  • 4.
  • 8. Rapid technology change, applications growth
  • 11.
  • 12. Swiss Army Knife of NGS Analysis SDK Intuitive GUI Traditional Bioinformatics Visualization Desktop Solutions EnterpriseSolutions High Performance File Format Conversion Tools Integration Epigenomics Transcriptomics Genomics RNA-Seq miRNA Read Mapping De Novo Assembly SNP/DIP Detection CHIP-Seq
  • 13. Why not use free tools? Are tools free or “free”? Tools vs solutions True cost of ownership Ease of Use Tools integration Support
  • 14. Small RNA Analysis(in Beta soon) Identify and filter/trim adapters annotate using mirBASE and other resources - target species of interest Merge/group by mature, precursor/reference Fully integrated with expression analysis
  • 15. De Novo Assembler Human assembly of 38x Illumina paired-end CLC Quality equivalent to Abyss CLC: 7 hrs, 1 node, 42 Gbof RAM Abyss: 80 hrs, 21 nodes, 336 Gbof RAM Metagenomics Assembly METAHIT Dataset MH0041 40M 75bp paired end 3 hrs on desktop, 6 Gb RAM Higher N50 and Total Contig Size than Reported
  • 16. Viral Sequencing at JCVI(See Nadia Fedorova’s Poster!) Amplify and Barcode using SISPA, 454 + Illumina Sequencing Depth of coverage sometimes >1000x De novo Assembly of Consensus for all Segments For each segment: Map reads from each technology independently using best full length reference from NCBI, call variations Update reference with variations confirmed by multiple technologies Map reads using updated reference and all reads Convert to consed, analyze, order Sanger closure reactions Source: Jessica Hostetler, Nadia Federova, Tim Stockwell, Danny Katzel
  • 17. Why CLC bioTools? CLC handled hybrid sequencing technologies directly Very biased coverage confounded other assemblers that expect random arrival stats.  CLC didn’t seem to suffer from biased coverage.  Very accurate SNP calls in areas of deep coverage. Tim Stockwell Director of Viral Informatics J. Craig Venter Institute
  • 18. Targeted Resequencing QC Assessment of targeted sequencing technology Coverage Statistics for Targeted Regions Very short schedule, limited bioinformatics staff Plug-in development leveraging CLC tools to automate the process and meet short deadline QC Report now available as plug-in
  • 19. Professional Services Developing customized solutions Integration with LIMS, workflows, DB Bioinformatics Algorithm Development Cloud and Grid Integration Data Analysis
  • 20. Questions? Saul A. Kravitz, PhD skravitz@clcbio.com (301)355-0813 Thank you for listening
  • 21. Questions Saul A. Kravitz, PhD skravitz @ clcbio.com 301)355-0813 Thank you for listening

Editor's Notes

  1. GUI-driven tools and workflows
  2. - miRNA workflow leveraging mirBASE and other resources
  3. Very fast, small memory footprint
  4.    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.
  5. 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*