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March 30, 2020
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Computational Approaches for Optimized Nanopore Sequencing Workflows


This webinar features two speakers who will discuss novel computational approaches to optimize sequencing workflows on Oxford Nanopore sequencing platforms.

Our first speaker, Jonathan Foox of the Institute for Computational Biomedicine at Weill Cornell Medicine, will review the rapidly evolving landscape of software to interpret raw Nanopore current data and report modified bases. He will review commonly used and newly available algorithms, and describe the advantages, challenges, and limitations of each. He will also compare base modification call sets generated from Nanopore data against call sets from short-read bisulfite data, as part of the Epigenomics Quality Control study, which aims to describe the reproducibility of genome-wide methylation calling and provide a benchmark of base modification detection across sequencing platforms and library types.

Our second speaker, Miten Jain of the University of California, Santa Cruz, will demonstrate an optimized PromethION nanopore sequencing method that sequenced eleven human genomes on one machine in nine days, using just three flow cells per sample. He will describe computational tools that his team used for this project: Shasta, a de novo long read assembler; and MarginPolish & HELEN, a suite of nanopore assembly polishing algorithms. Dr. Jain will also discuss an evaluation of assembly performance for diploid, haploid, and trio-binned human samples in terms of accuracy, cost, and time and demonstrate improvements relative to current state-of-the-art methods in all areas. He will also discuss how the addition of proximity ligation (Hi-C) sequencing yielded near chromosome-level scaffolds for all eleven genomes.

This webinar is part of the 2020 GenomeWeb/Association of Biomolecular Resource Facilities webinar series, which highlights methods, techniques, and instrumentation that support life science research.

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