Christopher T. Saunders

Aardvark: Sifting through differences in a mound of variants

Aardvark benchmarks genomic variant calling accuracy by comparing haplotype sequences with a basepair score, supporting multiple variant types and outperforming hap.py.

Portello: Making global assembly more effective for rare-disease whole genome sequencing

Portello improves variant calling accuracy in rare-disease whole genome sequencing by aligning de novo assembly contigs to a reference genome, reducing basecall errors and enabling better interpretation of complex loci.

LCSKPOA: Enabling banded semi-global partial order alignments via efficient and accurate backbone generation through extended lcsk++

The paper introduces an extended LCSk++ algorithm for graph-based alignment, improving memory and runtime efficiency for local and semi-global POA while maintaining alignment quality.

Complex structural variant visualization with SVTopo

SVTopo visualizes complex structural variants using high-accuracy long reads, providing clear figures to understand multi-breakpoint events in human genomes.

The Platinum Pedigree: A long-read benchmark for genetic variants

The paper creates a long-read benchmark for genetic variants using a large pedigree, improving variant calling performance and introducing new truth sets for tandem repeats and structural variants.

Sawfish: Improving long-read structural variant discovery and genotyping with local haplotype modeling

Sawfish improves long-read structural variant calling accuracy by modeling local haplotypes, outperforming existing tools in benchmark tests and joint-genotyping analyses.

Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition

Pooling Fiber-seq gDNA with concatenated MAS-Seq cDNA in one PacBio run gives phased genome, methylome, chromatin, and transcriptome, exposing four gene disruptions from one X;13 translocation.

A Murine Database of Structural Variants Enables the Genetic Architecture of a Spontaneous Murine Lymphoma to be Characterized

The paper creates a database of structural variants in 40 inbred mouse strains and identifies an SV linked to lymphoma susceptibility in SJL mice.

StarPhase: Comprehensive Phase-Aware Pharmacogenomic Diplotyper for Long-Read Sequencing Data

StarPhase diplotypes 21 pharmacogenes using long-read sequencing with high accuracy, updating 26.2% of existing diplotypes and highlighting gaps in pharmacogenomic databases.

Long-Read Sequencing Increases Diagnostic Yield for Pediatric Sensorineural Hearing Loss

This study evaluates the diagnostic yield of long-read sequencing in pediatric sensorineural hearing loss, finding it detects structural variants missed by short-read sequencing.

RFC1 repeat expansion analysis from whole genome sequencing data simplifies screening and increases diagnostic rates

The paper develops a whole genome sequencing method to detect RFC1 repeat expansions, improving diagnostic rates and simplifying the workflow for cerebellar ataxia diagnosis.

Direct haplotype-resolved 5-base HiFi sequencing for genome-wide profiling of hypermethylation outliers in a rare disease cohort

The paper uses HiFi sequencing to identify hypermethylation outliers in a rare disease cohort, finding allele-specific loss of regulatory elements linked to disease.

HiPhase: Jointly phasing small and structural variants from HiFi sequencing

HiPhase jointly phases small and structural variants from HiFi sequencing, achieving improved phase block NG50 and gene phasing rates.

REViewer: Haplotype-resolved visualization of read alignments in and around tandem repeats

REViewer visualizes sequencing data around long repeat expansions by reconstructing haplotypes and aligning reads, improving the assessment of repeat genotype calls and detecting interruptions.

Strelka2: Fast and accurate variant calling for clinical sequencing applications

Strelka2 is a variant calling tool that improves accuracy and reduces compute cost for germline and somatic variant detection in clinical sequencing.

Manta: Rapid detection of structural variants and indels for clinical sequencing applications

Manta rapidly detects structural variants and indels in clinical sequencing by optimizing speed and accuracy for germline and somatic analysis.