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CSU IDRC Next Generation Sequencing Core Genomic Sequencing Services

CSU IDRC Next Generation Sequencing Core Genomic Sequencing Services. Semiconductor DNA Sequencing. Ion Proton. Ion Torrent. “Sequencing on a Chip”. Semiconductor Sequencing in a Nutshell. “It’s a computational pH meter”. Metagenomics. Environmental samples of communities of organisms

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CSU IDRC Next Generation Sequencing Core Genomic Sequencing Services

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  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. 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 = 1014 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 Strong scaling • 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

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

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