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

The use of the human reference genome has shaped methods and data across modern
genomics. This has offered many benefits while creating a few constraints. In the following …

Recently, Gagie et al. proposed a version of the FM-index, called the r-index, that can store
thousands of human genomes on a commodity computer. Then Kuhnle et al. showed how to …

Mapping of high-throughput sequencing (HTS) reads to a single arbitrary reference genome
is a frequently used approach in microbial genomics. However, the choice of a reference …

The reference genome serves two distinct purposes within the field of genomics. First, it
provides a persistent structure against which findings can be reported, allowing for universal …

Motivation: As high-throughput sequencing (HTS) technology becomes ubiquitous and the
volume of data continues to rise, HTS read alignment is becoming increasingly rate-limiting …

Genome graphs allow very general representations of genetic variation; depending on the
model and implementation, variation at different length-scales (single nucleotide …

Abstract Gagie, Navarro and Prezza's r-index (SODA, 2018) promises to speed up DNA
alignment and variation calling by allowing us to index entire genomic databases, provided …

Short-read aligners predominantly use the FM-index, which is easily able to index one or a
few human genomes. However, it does not scale well to indexing collections of thousands of …

The current standard practice for assembling individual genomes involves mapping millions
of short DNA sequences (also known as DNA 'reads') against a pre-constructed reference …