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Challenges and opportunities of new sequencing technologies

Challenges and opportunities of new sequencing technologies. Dan Lawson BRC 2011 – Annual Meeting UT Southwestern Medical Center Dallas, TX 26-27 September 2011. Challenges and opportunities of new sequencing technologies. Challenges. PATRIC. ViPR /IRD. EuPathDB. VectorBase.

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Challenges and opportunities of new sequencing technologies

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  1. Challenges and opportunities of new sequencing technologies Dan Lawson BRC 2011 – Annual Meeting UT Southwestern Medical Center Dallas, TX 26-27 September 2011

  2. Challenges and opportunities of new sequencing technologies

  3. Challenges PATRIC ViPR/IRD EuPathDB VectorBase

  4. Challenges & Opportunities of Next Gen Sequencing reference assemblies re-sequencing isolates/strains Assembly Metagenomics Comparative genomics Sequencing Population biology Scalability Archiving data Data visualization RNA-Seq BRC focus

  5. Opportunities, Challenges, & Impact of Next Generation Sequencing Technologies: GSCID perspective Matthew Henn Director of Viral Genomics, Broad Institute Jennifer Wortman Director Microbial Informatics, Broad Institute Granger Sutton Professor Informatics, JCVI

  6. Large number of genomes @ low cost Opportunity: large scale projects with comparative potential Challenges: • Analyses computationally intensive • Standardized analyses & reference selection • Draft quality versus finished quality • Genotype vs. phenotype correlations • Visualization across large datasets & groups of samples • Patient confidentiality Impacts: • Pangenome construction • Gene content/synteny analysis • Phylogenetic reconstruction • Time series analysis

  7. High Resolution Data from Multiple Platforms Opportunity: unprecedented sensitivity and specificity to detect sequence polymorphisms and genes Challenges: • Integration of data from multiple technologies • Read-based analysis • Computationally & storage intensive • need good read mapping to reference dbs • Visualization (genome -> read) • What data do you make available • Levels of availability/access • Data processing/QC steps Impacts: • SNP calling • Population Profiling (e.g. viral) • Assembly & Haplotype Reconstruction • Annotation

  8. Microbial Community Profiling Opportunity: Understanding community dynamics in health and disease,polymicrobialdiseases Challenge: • Exploratory (you don’t know what is there) • What data are important & need be compared (e.g. reads, assemblies, variatns, genes, etc.) • Read-based based analysis • Metadata standardization • Visualization Impacts: • Sequence many organisms in parallel • Profile community transcription • Comprehensive identification of community members/functions

  9. Challenges & Opportunities of Next Gen Sequencing reference assemblies re-sequencing isolates/strains Assembly Metagenomics Comparative genomics Sequencing Population biology Scalability Archiving data Data visualization RNA-Seq BRC focus

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