Sentieon DNAscope LongRead - A highly Accurate, Fast, and Efficient Pipeline for Germline Variant Calling from PacBio HiFi reads

Abstract

PacBio(R) HiFi sequencing is the first technology to offer economical and highly accurate long-read sequencing, with average read lengths greater than 10kb and average base accuracy of 99.8%1. Here, we present DNAscope LongRead, an accurate and efficient pipeline for germline variant calling from PacBio(R) HiFi reads. DNAscope LongRead is a modification and extension of Sentieons DNAscope tool, a precisionFDA award-winning variant caller. DNAscope LongRead is computationally efficient, calling variants from 30x HiFi samples in under 4 hours on a 16-core machine (120 virtual core-hours) and highly accurate, with precision and recall on the most recent GIAB benchmark dataset exceeding 99.83% for HiFi samples sequenced at 30x coverage, and robust to changes in benchmark dataset and upstream library preparation and sequencing.