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CSU IDRC Next Generation Sequencing Core Genomic Sequencing Services.

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Presentation on theme: "CSU IDRC Next Generation Sequencing Core Genomic Sequencing Services."— Presentation transcript:

1 CSU IDRC Next Generation Sequencing Core Genomic Sequencing Services

2 Semiconductor DNA Sequencing Ion Proton Ion Torrent “Sequencing on a Chip”

3 Semiconductor Sequencing in a Nutshell “It’s a computational pH meter”

4 Metagenomics Environmental samples of communities of organisms water, soil samples human & animal microbiomes mine tailings, oil spills deep sea, polar ice etc.

5 Metagenomics Pipeline CSU Cray supercomputer; Oak Ridge Titan supercomputer Torrent/Proton sequencers Megan NCBI nucleotide databases

6 Metagenomics Tools Ion Proton Sequencer In: Sample DNA Out: 50M DNA fragments NCBI nucleotide database DNA fragments 15M+ records Do the math: 50M * 15M = queries mpiBLAST Highly parallelized Blast algorithm NGS sample DNA Query NCBI DB CSU Cray XT6m 2,016 CPU cores

7 Metagenomics Dr. Toni Piaggio, National Wildlife Research Center, Fort Collins Florida Everglades water samples (4) “What species are in the water?” CSU NextGen Sequencing Core: Ion Proton; 2 weeks CSU Cray: 1,000 cores, 24-hours, 4 runs; 1 week Results

8 Metagenomics Rarefaction curves Estimate species richness Asymptotic? Find rare species

9 Computational Resources Oak Ridge Titan Cray XK7 Supercomputer 300K CPU cores; 50M GPU cores mpiBlast NCBI nucleotide DB Query 100% of sample DNA CSU Cray XT6m Supercomputer 2,016 CPU cores mpiBlast NCBI nucleotide DB Query 1% of sample DNA Strong scaling

10 Summary Big Data Issues Semiconductor sequencer data Large-scale database queries High-performance computing


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