Wouter De Coster

This study evaluates the diagnostic value of long-read genome sequencing in DEE patients, finding it particularly effective for resolving complex structural variants not detected by short-read sequencing.

The paper analyzes somatic mutations in neurons from FTLD-TDP type C patients and controls, finding extensive low-frequency variants in TARDBP and other genes.

This paper benchmarks 7 TR genotyping tools using Nanopore long-read data, finding that no single tool is best across all metrics, and that sequence-level accuracy is crucial for clinical and population studies.

inqiSTR is a toolkit for efficient and accurate tandem repeat genotyping from long-read sequencing data, enabling population-scale analysis and downstream applications.

This study identifies distinct TAF15 amyloid filament structures in different FTLD-FET subtypes, leading to the renaming of the disease group as FTLD-TAF15.

The paper characterizes ANXA11 proteinopathy in FTLD-PLS and MND-TDP cases, showing it is common in FTLD-PLS but not linked to pathogenic ANXA11 variants or TDP type C.

This study identifies genetic risk factors for FTLD-TDP subtypes using whole-genome sequencing and meta-analysis across multiple cohorts.

Methylmap visualizes modified nucleotide frequencies across positions for large sample cohorts using standardized BAM/CRAM files.

This study uses long-read sequencing and optical genome mapping to fully characterize unresolved structural variants, achieving single-basepair resolution and improving diagnostic yield.

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 PathSTR, a tool for analyzing tandem repeats using long-read sequencing, and demonstrates its application in a Myotonic Dystrophy type 1 case.

Scywalker provides a scalable analysis pipeline for nanopore single-cell transcriptome data, showing good correlation with short-read analyses and enabling isoform-level cell-type-specific expression identification.

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

NanoPack2 provides tools for evaluating long-read sequencing data at scale, with updates to the NanoPack software suite.

The paper introduces methplotlib, a tool for visualizing and analyzing modified nucleotides from nanopore sequencing data, along with scripts for statistical analysis.

This paper develops a method to accurately characterize expanded tandem repeats using long-read sequencing on PromethION, outperforming traditional methods and enabling clinical applications.

The paper benchmarks structural variant calling tools using Oxford Nanopore PromethION sequencing of the human genome, finding Minimap2 and Sniffles to be the most accurate and efficient.

This study determines the optimal read length for structural variant discovery and haplotyping using long-read sequencing in human genomes.

NanoPack bundles Python3 tools (command line, GUI, web service) for QC plotting, summary statistics, read filtering and contaminant removal of Oxford Nanopore and PacBio long reads.