It has been over a decade since the first publication of a method dedicated entirely to
mapping long-reads. The distinctive characteristics of long reads resulted in methods …

Abstract Here the Human Pangenome Reference Consortium presents a first draft of the
human pangenome reference. The pangenome contains 47 phased, diploid assemblies …

The short arms of the human acrocentric chromosomes 13, 14, 15, 21 and 22 (SAACs) share
large homologous regions, including ribosomal DNA repeats and extended segmental …

Pangenome graphs can represent all variation between multiple genomes, but existing
methods for constructing them are biased due to reference-guided approaches. In response …

Motivation Sequence alignment is a memory bound computation whose performance in
modern systems is limited by the memory bandwidth bottleneck. Processing-in-memory …

Sequence alignment remains a fundamental problem in computer science with practical
applications ranging from pattern matching to computational biology. The ever-increasing …

In the last years, advances in genome sequencing technologies have enabled the
proliferation of genomic applications that guide personalized medicine. These applications …

Nanopore sequencing is a widely-used high-throughput genome sequencing technology
that can sequence long fragments of a genome into raw electrical signals at low cost …

Motivation Pairwise sequence alignment is a very time-consuming step in common
bioinformatics pipelines. Speeding up this step requires heuristics, efficient implementations …

Motivation Efficiently aligning sequences is a fundamental problem in bioinformatics. Many
recent algorithms for computing alignments through Smith–Waterman–Gotoh dynamic …