Fritz Joachim Sedlazeck

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

The paper identifies novel structural variants in Han Chinese genomes using long-read sequencing and links them to phenotypic diversity and disease susceptibility.

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 uses long-read sequencing data to analyze STR variability across 2,645 individuals, identifying disease-associated STR loci with elevated allelic variability and introducing the PLVI metric.

The paper uses long-read sequencing to identify structural variants and their impacts on gene expression and methylation in diverse human brain samples.

The paper uses long-read sequencing on 100 samples from the 1000 Genomes Project to identify structural variants and improve understanding of human genetic variation.

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.

The paper introduces genomic stratifications for human reference genomes GRCh37, GRCh38, and T2T-CHM13v2.0 to benchmark variant caller performance in difficult regions.

This paper presents a long-read sequencing dataset of cancer samples, showing its ability to resolve structural variants, haplotypes, and methylation patterns in precision medicine.

StratoMod predicts variant calling errors using interpretable machine learning to help design better variant calling pipelines.

The paper compares single-cell whole genome amplification methods and reference genomes for detecting somatic copy number variants in human brain tissue.

STIX annotates structural variants using long-read data, achieving high accuracy and identifying common SVs in population-scale datasets.

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.

The paper introduces NAHRwhals, a method to detect serial structural variations in long-read genomes, identifies 37 sSV loci in humans, and shows their relevance to disease.

MethPhaser improves haplotype phasing by using methylation signals from Oxford Nanopore data, increasing phase length N50 by 3-fold with minimal error increase.

The paper investigates how different genome references affect inversion detection, showing that T2T-CHM13 and long-read sequencing improve resolution of challenging inversions.

This paper shows that using a complete reference genome improves the accuracy and reduces false positives in detecting structural variants in cancer genomes.

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.

The paper compares short-read and long-read sequencing in the All of Us initiative, finding HiFi reads provide the most accurate variant calling and presents a cloud-based pipeline for long-read analysis.

Sniffles2 improves SV detection accuracy and speed, enabling mosaic and population-level SV calling with applications in neurological disorders.

DRAGEN provides fast and accurate genome analysis across 3,202 genomes, outperforming existing methods in variant detection speed and accuracy for various types including SNV, indel, STR, SV, and CNV.

The paper introduces levioSAM2, a method for accurate lift-over between genome assemblies, improving variant calling accuracy when mapping to older references.

The paper benchmarks small and large variants in tandem repeats across 86 samples, creating a benchmark dataset and comparison method for TR variant calling.

The paper investigates DUP-TRP/INV-DUP genomic rearrangements in neurodevelopmental disorders, identifying four SV haplotypes and refining template switching points using multiple sequencing technologies.

The paper presents the complete sequence of a human Y chromosome, correcting errors in the GRCh38 reference and adding over 30 million base pairs.

The paper introduces a pangenome research toolkit to analyze complex genomic variations across multiple scales, improving the interpretation of repetitive and clinically relevant genes.

The paper introduces TRGT, a tool for tandem repeat genotyping, and a database of 937,122 TRs across 100 genomes, achieving high concordance and detecting repeat expansions, methylation, and mosaicism.

The paper introduces the EN-TEx resource, which provides personal epigenomes and variant-impact models across multiple tissues, revealing allele-specific loci and their associations with GWAS loci.

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.

This paper develops a scalable protocol for Oxford Nanopore long-read sequencing, achieving high SNP and structural variant detection with haplotype-resolved methylation calls, suitable for large-scale genomics projects.