Donald N. Freed

The paper introduces DNAscope Hybrid, a pipeline combining short and long-read sequencing for improved variant calling accuracy and efficiency.

The paper introduces and benchmarks DNAscope LongRead and Hybrid pipelines for variant calling on ONT data, showing high accuracy and efficiency in SNP, Indel, and Structural Variant detection.

The paper creates a variant benchmark for X and Y chromosomes using a complete assembly of HG002, highlighting challenges in variant detection in complex regions.

The paper introduces the Sentieon ctDNA pipeline for accurate and efficient small somatic variant calling from ctDNA sequencing data, showing improved accuracy over existing methods.

DNAscope LongRead is a pipeline for germline variant calling from PacBio HiFi reads, achieving high accuracy and efficiency in variant detection.

DNAscope improves small variant calling accuracy and reduces computational cost compared to DNAseq using a machine-learned genotyping model.

A haplotype-based somatic variant caller paired with a machine learning filter, reported as more accurate than other callers on in-silico mixtures of GIAB reference samples.

Sentieon's rewrite of GATK and MuTect pipelines runs on average 36x faster than GATK Best Practices on public human data while matching its calls (average F-score 0.9996).