CSU IDRC Next Generation Sequencing CoreGenomic 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• water, soil samples• human & animal microbiomes• mine tailings, oil spills• deep sea, polar ice• etc. etc.

Metagenomics Pipeline

CSU Cray supercomputer;Oak Ridge Titan supercomputer

Torrent/Protonsequencers Megan

NCBI nucleotide databases

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

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

Metagenomics

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

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

Summary

Big Data Issues

• Semiconductor sequencer data

• Large-scale database queries

• High-performance computing