Trevor Pesout

The paper introduces Minigraph-Cactus, a pangenome pipeline that constructs pangenome graphs directly from whole-genome alignments, demonstrating improved performance in mapping and variant calling across human and Drosophila data.

The paper presents a draft human pangenome reference that improves variant discovery and structural variant detection compared to existing references.

The paper shows recombination between heterologous human acrocentric chromosomes using pangenome data, revealing pseudo-homologous regions linked to Robertsonian translocations.

This paper develops a scalable protocol for Oxford Nanopore long-read sequencing, achieving high SNP and structural variant detection with haplotype-resolved methylation calls, suitable for large-scale genomics projects.

The paper evaluates sequencing and assembly methods to create high-quality diploid human genome assemblies, finding that long reads and haplotype sorting improve accuracy and completeness.

The paper evaluates variant calling in difficult genomic regions using short- and long-read sequencing, showing improved performance with new methods and multi-technology approaches.

The paper introduces a haplotype-aware variant calling pipeline for nanopore and PacBio HiFi data, achieving high accuracy in variant detection and de novo assembly polishing.

The paper summarizes methods and lessons from assembling 16 vertebrate genomes, highlights the importance of long-read sequencing, and introduces the Vertebrate Genomes Project to generate complete reference genomes for all vertebrate species.

The paper presents an optimized PromethION nanopore sequencing method and new computational tools for efficient human genome assembly, achieving high accuracy and speed.

This paper introduces a haplotype-aware genotyping method for noisy long reads, showing improved accuracy in variant calling using longer reads from Oxford Nanopore and Pacific Biosciences.