CSU IDRC Next Generation Sequencing Core

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CSU IDRC Next Generation Sequencing Core Genomic
Sequencing Services
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Semiconductor DNA Sequencing
Ion Proton
Ion Torrent
Sequencing on a Chip
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Semiconductor Sequencing in a Nutshell
Its a computational pH meter
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Metagenomics

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

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

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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

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Metagenomics

• Rarefaction curves
• Estimate species richness
• Asymptotic?
• Find rare species

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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

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Summary

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