DAN LAWSON BRC 2011 – ANNUAL MEETING UT SOUTHWESTERN MEDICAL CENTER DALLAS, TX SEPTEMBER 2011 Challenges and opportunities of new sequencing technologies

Challenges PATRICViPR/IRD EuPathDB VectorBase

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

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 BRC Annual Mtng Session #2: GSCID Perspectives on Next Gen. Tech. Henn, Wortman, & Sutton

Large number of 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 BRC Annual Mtng Session #2: GSCID Perspectives on Next Gen. Tech. Henn, Wortman, & Sutton

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 BRC Annual Mtng Session #2: GSCID Perspectives on Next Gen. Tech. Henn, Wortman, & Sutton High Resolution Data from Multiple Platforms

Opportunity: Understanding community dynamics in health and disease, polymicrobial diseases 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 BRC Annual Mtng Session #2: GSCID Perspectives on Next Gen. Tech. Henn, Wortman, & Sutton Microbial Community Profiling

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