SCRIPPS INSTITUTION OF OCEANOGRAPHY BIOLOGY SECTION RESEARCH CANDIDATE SEMINAR
DATE: October 16th, Monday, 10am
LOCATION: Hubbs Hall 4500
SPEAKER: Todd Michael, Ph.D.
J. Craig Venter Institute
TITLE: Next generation genomics and epigenomics at the bench or at sea with nanopore sequencing
Advances in sequencing, specifically short read sequencing, have created unprecedented opportunities to explore novel organisms, populations and environments. However, these sequencing platforms require large capital expenditures, compute systems and investment per experiment. Nanopore sequencing, which is considered the “holy grail” of sequencing, has now addressed many of these limitations and even enhanced the scope of opportunities with ultra-long reads, direct RNA sequencing and DNA/RNA base modification detection. The Oxford Nanopore MinION sequencer is the size of a USB memory stick, only requires a laptop to run, generates up to 20 gigabases of ultra-long sequence (reads up to 1 megabase to date) per flowcell, enables ultra-fast amplicon sequencing (20 min), and complete (closed circles) bacterial genome sequencing/assembly in under an hour. The small size, affordable price and modest compute requirements means that researchers can sequence their plasmid at the bench or their ocean floor sediment on a research vessel. I will discuss how my group has been using the Oxford Nanopore MinION to generate platinum quality reference genomes and my plans to leverage this system in kelp genomics.