Motivation: Whole-genome high-coverage sequencing has been widely used for personal
and cancer genomics as well as in various research areas. However, in the lack of an …

Many disciplines, from human genetics and oncology to plant breeding, microbiology and
virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes …

We propose a generic approach to replace the canonical sequence representation of
genomes with graph representations, and study several applications of such extensions. We …

Although much is known about human genetic variation, such information is typically
ignored in assembling new genomes. Instead, reads are mapped to a single reference …

The increasing availability of high-throughput sequencing technologies has led to
thousands of human genomes having been sequenced in the past years. Efforts such as the …

Until recently, genomics has concentrated on comparing sequences between species.
However, due to the sharply falling cost of sequencing technology, studies of populations of …

Computational pan-genome analysis has emerged from the rapid increase of available
genome sequencing data. Starting from a microbial pan-genome, the concept has spread to …

Motivation: Next-generation sequencing (NGS) has revolutionized biomedical research in
the past decade and led to a continuous stream of developments in bioinformatics …

The comprehensive discovery of structure variations (SVs) is fundamental to many genomics
studies and high-throughput sequencing has become a common approach to this task …

Completely sequencing genomes is expensive, and to save costs we often analyze new
genomic data in the context of a reference genome. This approach distorts our image of the …