Abstract The Telomere-to-Telomere consortium recently assembled the first truly complete
sequence of a human genome. To resolve the most complex repeats, this project relied on …

Human genomes are typically assembled as consensus sequences that lack information on
parental haplotypes. Here we describe a reference-free workflow for diploid de novo …

Polymorphic inversions are ubiquitous in humans and they have been linked to both
adaptation and disease. Following their discovery in Drosophila more than a century ago …

Haplotype information is crucial for biomedical and population genetics research. However,
current strategies to produce de novo haplotype-resolved assemblies often require either …

Conservation genomics aims to preserve the viability of populations and the biodiversity of
living organisms. Invertebrate organisms represent 95% of animal biodiversity; however, few …

Motivation Strand-seq is a specialized single-cell DNA sequencing technique centered
around the directionality of single-stranded DNA. Computational tools for Strand-seq …

Motivation Current sequencing technologies are able to produce reads orders of magnitude
longer than ever possible before. Such long reads have sparked a new interest in de novo …

The prevailing genome assembly paradigm is to produce consensus sequences that
“collapse” parental haplotypes into a consensus sequence. Here, we leverage the …

Accurate reference genome sequences provide the foundation for modern molecular
biology and genomics as the interpretation of sequence data to study evolution, gene …

Haplotype information is crucial for biomedical and population genetics research. However,
current strategies to produce de-novo haplotype-resolved assemblies often require either …