Over the past few years, many tools have been developed to enable comprehensive variant detection from PacBio HiFi reads. This talk describes a flexible, modular workflow for variant detection and prioritization from HiFi whole-genome sequencing data, including open-source tools for quality control, alignment, small variant detection, and phasing, structural variant detection, genotyping of tandem repeats, and de novo assembly. This pipeline is available on GitHub as a Snakemake workflow and has been adapted into a Cromwell WDL workflow by Microsoft Genomics.
May 17, 2021 | Presentation