Fritz Joachim Sedlazeck

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

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

The paper shows that spontaneous structural rearrangements in F1 offspring of Brassica napus hybrids lead to rapid genome diversification and phenotypic variation.

This study identifies 3,154 high-confidence structural variants in Parkinson's disease using short-read sequencing and validates some with long-read data, highlighting limitations of short-read methods.

The paper uses long-read sequencing to analyze genetic polymorphisms in 370 medically relevant genes across 41 individuals from 19 populations, identifying CNVs and variants missed by short-read sequencing.

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.

The paper presents two methods to accurately detect GBA variants and reciprocal recombinants, showing higher GBA variant frequency in Lewy body dementia compared to Parkinson's disease.

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.

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

The paper evaluates variant calling in difficult genomic regions using short- and long-read sequencing, showing improved performance with new methods and multi-technology approaches.

Read2Tree processes raw sequencing reads to build phylogenetic trees, outperforming conventional methods in speed and accuracy across diverse datasets.

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

The T2T-CHM13 reference genome improves read mapping and variant calling across diverse samples, reducing false positives and enabling novel variant discovery.

Variabel identifies low frequency intra-host variants from Oxford Nanopore sequencing data, outperforming existing tools for this task.

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 presents an improved chromosome-scale genome assembly for the Syrian hamster using long-read sequencing, resulting in higher continuity and gene annotation accuracy.

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

This paper presents STRspy, a method for accurate STR profiling using nanopore sequencing, achieving 100% concordance with validated genotypes and identifying flanking SNPs with >90% accuracy.

This paper demonstrates that sequencing short DNA molecules with nanopore sequencing improves copy number inference in cancer, offering higher sensitivity and accuracy compared to traditional methods.

Vulcan improves long-read mapping and structural variant calling by using dual-mode alignment, enhancing accuracy for Oxford Nanopore Technology reads.

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.

SVCollector selects an optimal subset of individuals for long-read sequencing to maximize genetic diversity representation across subpopulations.

The paper presents a method to index and search raw alignments from thousands of samples to improve the classification of somatic and pathogenic structural variants.

SVhound predicts regions likely to contain novel structural variations by analyzing population-level SV datasets, showing high correlation with full datasets and applicability across species.

This study analyzes over 7,000 SARS-CoV-2 datasets to reveal genomic diversity, showing iSNVs and small indels drive variation, and highlights implications for qRT-PCR and transmission tracking.

This study uses rapid diagnostics and metatranscriptomics to analyze SARS-CoV-2 infection, revealing viral evolution, host responses, and drug interactions in NYC samples.

This study introduces nanoNOMe, a method combining NOMe-seq and nanopore sequencing to profile chromatin accessibility and methylation in human cell lines, revealing phased methylation, large-scale patterns, and structural variations.

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.

This study uses long-read sequencing to identify structural variants in breast cancer genomes, showing high accuracy and sensitivity compared to short-read methods.