Close Menu
March 30, 2020
Sponsored by
GenomeWeb/ABRF

Computational Approaches for Optimized Nanopore Sequencing Workflows

GenomeWebinar

Postdoctoral Associate in Computational Biomedicine, Institute for Computational Biomedicine at Weill Cornell Medicine

Research Scientist, University of California, Santa Cruz

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.

Sponsored by

Master's and doctoral students in the UK call on funding groups to extend their grants for the duration of the disruption caused by the COVID-19 outbreak, the Guardian reports.

Squid can make edits to their RNA within the cytoplasm of their axons, Science News reports.

The Chan Zuckerberg Initiative is putting $25 million toward COVID-19 treatment research, according to the Verge.

In Science this week: researchers engineer version of Cas9 that is nearly PAM-less, and more.

Mar
30
Sponsored by
GenomeWeb/ABRF

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

May
06
Sponsored by
Isoplexis

This webinar will discuss the application of single-cell proteomics and immune-imaging in adoptive cell therapy (ACT) for cancer.