Jesse Farek

This paper evaluates Illumina Constellation sequencing for rare disease research, showing it can detect structural variants and haplotype phasing with low DNA input and existing infrastructure.

Celeste provides a scalable cloud infrastructure for population-scale sequencing projects, including a variant-calling pipeline optimized for clinical variant detection.

xAtlas is a scalable variant caller for NGS data that provides faster and accurate SNV and indel detection compared to existing methods.

The paper introduces FixItFelix and a modified GRCh38 reference to improve variant calling and expression analysis in genes with reference errors, showing benefits across multiple sequencing types and populations.

This paper expands genome benchmarking to include difficult-to-map regions using linked and long reads, identifying more false negatives in variant calling.

This paper creates a comprehensive benchmark for challenging medically-relevant autosomal genes, improving variant recall from 8% to 100% by addressing reference-specific false duplications.

The paper develops a diploid assembly-based benchmark for variants in the MHC region using HG002 data, identifying 21496 small variants with high concordance to clinical HLA types.