Computational pangenomics is an emerging research field that is changing the way
computer scientists are facing challenges in biological sequence analysis. In past decades …

The significant decline in the cost of genome sequencing has dramatically changed the
typical bioinformatics pipeline for analysing sequencing data. Where traditionally, the …

Structural variants (SVs) account for a large amount of sequence variability across genomes
and play an important role in human genomics and precision medicine. Despite intense …

Given the popularity and elegance of k-mer-based tools, finding a space-efficient way to
represent a set of k-mers is important for improving the scalability of bioinformatics analyses …

k-mer-based methods are widely used in bioinformatics, but there are many gaps in our
understanding of their statistical properties. Here, we consider the simple model where a …

K-mer based methods have become prevalent in many areas of bioinformatics. In
applications such as database search, they often work with large multi-terabyte-sized …

A wave of technologies transformed sequencing over a decade ago into the high-throughput
era, demanding research in new computational methods to analyze these data. The …

De novo genetic variants are an important source of causative variation in complex genetic
disorders. Many methods for variant discovery rely on mapping reads to a reference …

Genotyping is a core application of high-throughput sequencing. We present KAGE, a
genotyper for SNPs and short indels that is inspired by recent developments within graph …

We present a new method and software tool called rowbowt that applies a pangenome
index to the problem of inferring genotypes from short-read sequencing data. The method …