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Past Presentations
Beyond the Reference: How Long Read Low Pass and Pangenomes are Shaping the Future of Genomics Across the Tree of Life
Alex Harkess, PhD
Long-read sequencing is no longer limited to well-funded model organism programs. This presentation covers how LRLP sequencing unlocks genomics across the full tree of life — from microbes to complex polyploid crops and animals — and how pangenomes are replacing linear references to better represent structural variation.
How LRLP sequencing makes long-read accessible and deployable at population scale
Why pangenomes outperform linear references for structural variant representation
Long-read low-pass applications in plant and animal breeding programs
Improved genotyping accuracy using pangenome-based imputation scaffolds
A Cost-Effective Pangenome-Based Platform for Genotype Imputation, QTL Mapping, and Selection Support in Plant and Animal Genomics
Standard genotyping approaches leave researchers choosing between affordability and data quality. This presentation introduces a pangenome-based platform that closes that gap — enabling high-resolution imputation, QTL detection, and genomic selection at population scale without the cost of full WGS.
How pangenome graphs unlock structural variation that linear references miss
Cost-effective genotyping for breeding programs using long-read low-pass sequencing
QTL mapping and selection support across plant and animal species
Real-world case studies demonstrating imputation accuracy improvements
Josh Clevenger, PhD
Polyploid crop genomes are among the most challenging in plant genomics. This PAG presentation walks through how long-read low-pass sequencing and CiFi-adapted scaffolding are solving two persistent problems: scalable genotyping in polyploids and assembly recovery when standard Hi-C approaches fail.
Long-read low-pass sequencing for cost-effective genotyping in polyploid crops
Pangenome reference construction using KhufuPAN and reference-based scaffolding
CiFi as a rescue strategy for difficult genome assemblies
QTL identification for phenological traits using the QTLVar pipeline
Blueberry Pangenomics and CiFi Assembly for Complex Polyploid Genomes
Kendall Lee, PhD
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