Ginger Metcalf

Himito: a Graph-based Toolkit for Mitochondrial Genome Analysis using Long Reads

Himito is a graph-based toolkit for analyzing mitochondrial genomes using long reads, achieving superior performance in assembly and variant calling and revealing age-related patterns in the All of Us dataset.

Evolutionary dynamics of Respiratory Syncytial Virus in pre-pandemic, pandemic, and post-pandemic periods in Houston, Texas, USA

This study analyzes RSV evolutionary dynamics across pre-pandemic, pandemic, and post-pandemic periods in Houston, finding reduced diversity during the pandemic and increased non-synonymous mutations in RSV/B.

K-mer analysis of long-read alignment pileups for structural variant genotyping

This paper introduces a method called kanpig for accurately genotyping structural variants using long-read alignment pileups, achieving higher concordance than existing tools.

Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk

The paper introduces a CN caller for KIV-2 repeats using short reads, showing high accuracy and demonstrating its correlation with Lp(a) levels and population-specific CN distributions.

Complete Genomic Characterization of Global Pathogens, Respiratory Syncytial Virus (RSV), and Human Norovirus (HuNoV) Using Probe-based Capture Enrichment.

This paper presents a probe-based capture enrichment method to obtain full-length genomes of RSV and HuNoV from clinical samples, achieving high completeness and improving variant tracking.

A common flanking variant is associated with enhanced meiotic stability of the FGF14-SCA27B locus

The paper identifies a common flanking variant linked to increased meiotic stability at the FGF14-SCA27B repeat locus.

Closing the gap: Solving complex medically relevant genes at scale

The paper introduces a targeted sequencing framework, TADGP, that accurately calls variants in complex medically relevant genes at lower cost than HiFi-WGS, enabling scalable analysis of dark genomic regions.

Examining intra-host genetic variation of RSV by short read high-throughput sequencing

The paper analyzes intra-host RSV genetic variation using short-read sequencing, finding low variation but differences between genomic and transcriptomic data.

Structural variation across 138,134 samples in the TOPMed consortium

The paper presents a comprehensive catalog of structural variants across 138,134 individuals, identifying novel variants and their associations with cardio-metabolic and hematologic traits.

xAtlas: Scalable small variant calling across heterogeneous next-generation sequencing experiments

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

Truvari: Refined Structural Variant Comparison Preserves Allelic Diversity

Truvari improves structural variant comparison by preserving allelic diversity, reducing allele frequency inflation compared to other methods.

A pan-genome approach to decipher variants in the highly complex tandem repeat of LPA

The paper uses a pan-genome graph approach to identify variation within the KIV-2 tandem repeats of the LPA gene across 47 haplotype-resolved assemblies.

Whole genome sequencing as an investigational device for return of hereditary disease risk and pharmacogenomic results as part of the All of Us Research Program

The paper describes the process of obtaining an FDA IDE for returning genomic results via WGS in the All of Us Research Program and presents validation results.

Fully resolved assembly of Cryptosporidium parvum

The paper presents a high-quality, complete reference genome for Cryptosporidium parvum using Oxford Nanopore and Illumina reads, enabling comprehensive genomic studies.

Whole genome sequencing identifies common and rare structural variants contributing to hematologic traits in the NHLBI TOPMed program

Oligonucleotide Capture Sequencing of the SARS-CoV-2 Genome and Subgenomic Fragments from COVID-19 Individuals

This study develops an oligonucleotide capture sequencing method to generate SARS-CoV-2 genomic and transcriptome sequences from clinical samples, revealing differential transcriptional activity and ORF10 expression.

Multiethnic catalog of structural variants and their translational impact for disease phenotypes across 19,652 genomes

The paper catalogs structural variants across 19,652 genomes and identifies their associations with proteomic measurements and disease phenotypes.