Low-cost whole-genome assembly has enabled the collection of haplotype-resolved
pangenomes for numerous organisms. In turn, this technological change is encouraging the …

De novo assembly of a human genome using nanopore long-read sequences has been
reported, but it used more than 150,000 CPU hours and weeks of wall-clock time. To enable …

The nematode Caenorhabditis elegans has shed light on many aspects of eukaryotic
biology, including genetics, development, cell biology, and genomics. A major factor in the …

Pangenomes provide access to an accurate representation of the genetic diversity of
species, both in terms of sequence polymorphisms and structural variants (SVs). Here we …

Haplotype-resolved or phased genome assembly provides a complete picture of genomes
and their complex genetic variations. However, current algorithms for phased assembly …

Genome graphs can represent genetic variation and sequence uncertainty. Aligning
sequences to genome graphs is key to many applications, including error correction …

Abstract Motivation De Bruijn graphs can be constructed from short reads efficiently and
have been used for many purposes. Traditionally, long-read sequencing technologies have …

Eukaryotic genome sequencing and de novo assembly, once the exclusive domain of well-
funded international consortia, have become increasingly affordable, thus fitting the budgets …

The commercial release of third-generation sequencing technologies (TGSTs), giving long
and ultra-long sequencing reads, has stimulated the development of new tools for …

Third-generation sequencing technologies from companies such as Oxford Nanopore and
Pacific Biosciences have paved the way for building more contiguous and potentially gap …