The exponential increase in sequencing data calls for conceptual and computational
advances to extract useful biological insights. One such advance, minimizers, allows for …

Processing large data sets has become an essential part of computational genomics.
Greatly increased availability of sequence data from multiple sources has fueled …

We present haplotype-resolved reference genomes and comparative analyses of six ape
species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan …

Motivation Given a string S, a minimizer scheme is an algorithm defined by a triple (k, w, 𝒪)
that samples a subset of k-mers (k-long substrings) from a string S. Specifically, it samples …

Motivation Sampling k-mers is a ubiquitous task in sequence analysis algorithms. Sampling
schemes such as the often-used random minimizer scheme are particularly appealing as …

Motivation A common method for analyzing genomic repeats is to produce a sequence
similarity matrix visualized via a dot plot. Innovative approaches such as StainedGlass have …

Streptococcus pneumoniae is an opportunistic human pathogen responsible for high
morbidity and mortality rates. Extensive genome sequencing revealed its large pangenome …

Whole genome duplication (WGD) is a powerful evolutionary mechanism in plants.
Autopolyploids have been comparatively less studied than allopolyploids, with sexual …

Genome sequences largely determine the biology and encode the history of an organism,
and de novo assembly—the process of reconstructing the genome sequence of an organism …

Sampling algorithms that deterministically select a subset of k-mers are an important
building block in bioinformatics applications. For example, they are used to index large …