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

Freed, D.; Rowell, W. J.; Wenger, A. M.; Li, Z.

doi:10.1101/2022.06.01.494452

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bioRxiv · 10.1101/2022.06.01.494452

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

Freed, D.·Rowell, W. J.·Wenger, A. M.·Li, Z.

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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.

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Freed, D., Rowell, W. J., Wenger, A. M., Li, Z.. 2022-06-03. Sentieon DNAscope LongRead - A highly Accurate, Fast, and Efficient Pipeline for Germline Variant Calling from PacBio HiFi reads. https://doi.org/10.1101/2022.06.01.494452

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