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

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

5. GUI-driven

6. HPC integration

7. Unprecedented data volumes

8. Rapid technology change, applications growth

9. Multi-platform data integration

10. No one-size-fits-all solutions

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