T2T Nanopore ultra-long workshop

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Join us, on-demand

4th April | 12pm – 4pm EDT

The generation of ultra-long reads using Oxford Nanopore Technologies (ONT-UL), with sequences extending beyond 100,000 bps, signifies a groundbreaking advancement in the field of genomics. ONT-UL data play a crucial role in Telomere-to-Telomere (T2T) hybrid assembly protocols, like Verkko, facilitating the assembly of complex genomic regions, spanning large structural variations, and offering comprehensive study of entire chromosomes.

Yet, generating this data poses significant challenges, including the careful preparation required to obtain intact, high-quality ultra-high molecular weight DNA and labor intensive loading of flow-cells, processes that have not yet been automated at scale. Moreover, the efficiency of producing ONT-UL data differs across various tissues and sample types, leading to variability in data quality among species, with some providing superior ultra-long sequences than others.

This open webinar was held on April 4th (12-4pm Eastern Time) to explore the nuances of ONT-UL data production and its application in ongoing T2T projects. We’ve gathered a panel of experts to share their insights on ONT-UL sequencing protocols, highlighting both breakthroughs and obstacles. Participants are invited to continue the conversation after the work in our T2T Slack Channel #ont-ul-troubleshooting and contribute to an open-access database of ONT-UL protocols to support the developer community.

Registration is now open to watch the session on demand. 

This webinar is supported by the UCSC Sequencing Technology Center, who leads ONT-UL production for the Human Pangenome Reference Consortium, and Oxford Nanopore Technologies

 

Speakers

Speaker's Name

Co-host

Karen Miga, Director, UCSC Sequencing Technology Center

Speaker's Name

Co-host

Adam Phillippy, Director and Senior Investigator Genome Informatics Section NHGRI / NIH

Speaker's Name

Ultra-long sequencing and development in Nottingham

Inswasti Cahyani (“Ninin”), School of Life Sciences, the University of Nottingham

Speaker's Name

Ultra-long Oxford Nanopore Technologies sequencing at UW

Kendra Hoekzema, University of Washington

Speaker's NameOxford Nanopore Technologies sequencing and development at UCSC

Brandy McNulty, UCSC Sequencing Technology Center

Speaker's NameThe utility of ultra-long reads in satellite DNA and T2T assemblies

Monika Cechova, UCSC

Speaker's Name

Ultra-long Oxford Nanopore Sequencing at NISC

Shelise Brooks, NISC/NIH Intramural Sequencing Center

Speaker's Name

Ultra-long Sequencing at the Vertebrate Genome Lab

Nivesh Jain, Vertebrate Genome Lab, The Rockefeller University

Patrick Grady

The Weird Genomes Rollercoaster: “Ultra”-long reads as the foundation of success in widely diverse assemblies

 

Patrick Grady, Colossal Biosciences

Speaker's Name

Crop genome sequencing challenges & opportunities

Alexander Wittenberg, KeyGene

Speaker's Name

Ultra-long sequencing experiences with a variety of mammalian sample types

Kristen Kuhn, USDA Meat Animal Research Center

Speaker's Name

The longer the better: optimizing read-length in non-human samples 

Sara Goodwin, NGS Core Director, CSHL

Speaker's NamePanelist

Sean McKenzie, Oxford Nanopore Technologies

Speaker's Name

Panelist

Jeannie Mounger, Oxford Nanopore Technologies

Speaker's NamePanelist

Androo Markham Oxford Nanopore Technologies

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Over the last decade, developments in extraction protocols and library preparation have significantly improved sequencing yields for ultra long protocols on Oxford Nanopore Sequencers. However, ultra long sequencing is still challenging dependent on sample and library preparation methods. We developed FindingNemo, a toolkit to optimize extractions and ultra-long library clean-up. The protocol can deliver >20 Gb of reads with an N50 > 100kb on a single MinION flow cell or >100Gb of reads on PromethION devices. The method works with multiple sequencing chemistries from R9.4 to R10.4 and, likely, beyond. Our comparisons show there are multiple routes to achieve ultra long library preparations and different approaches may help with challenging and complex samples. We also emphasize the importance of precise determination of input DNA amount through cell counting and quantification.

Nivesh is a molecular biologist leading ONT sequencing efforts at the Vertebrate Genome Lab and is an expert in U/HMW DNA extractions, Bionano optical mapping, and HiFi PacBio sequencing.

Patrick Grady obtained his PhD in Molecular & Cellular Biology under Rachel O’Neill's supervision at the University of Connecticut. His doctoral research centered on the genomic evolution of marsupials and developing bioinformatic techniques to improve telomere-to-telomere whole-genome comparisons.

Alongside his dissertation, Patrick collaborated with the CHM13-T2T Consortium to annotate repeats in the new human genome, developed algorithms to enhance nanopore sequencing analysis, contributed to the Ruminant T2T Consortium, and engaged in single-cell developmental biology research. His long-term goal is to leverage the power of complete T2T genomes alongside functional, epigenetic, and topological genomic data to answer complex evolutionary questions. At Colossal Biosciences, Patrick leads genome assembly projects involving species associated with extinct animals and contributes to functional genomics research with the Thylacine team.