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 …

DNA sequencing data continue to progress toward longer reads with increasingly lower
sequencing error rates. We focus on the critical problem of mapping, or aligning, low …

Abstract Motivation The Jaccard similarity on k-mer sets has shown to be a convenient proxy
for sequence identity. By avoiding expensive base-level alignments and comparing reduced …

High-throughput sequencing (HTS) technologies have revolutionized the field of genomics,
enabling rapid and cost-effective genome analysis for various applications. However, the …

The high execution time of DNA sequence alignment negatively affects many genomic
studies that rely on sequence alignment results. Pre-alignment filtering was introduced as a …

Motivation Pairwise sequence alignment is a heavy computational burden, particularly in the
context of third-generation sequencing technologies. This issue is commonly addressed by …

Seed design is important for sequence similarity search applications such as read mapping
and average nucleotide identity (ANI) estimation. Although k-mers and spaced k-mers are …

Horizontal gene transfer (HGT) phenomena pervade the gut microbiome and significantly
impact human health. Yet, no current method can accurately identify complete HGT events …

Computational complexity is a key limitation of genomic analyses. Thus, over the last 30
years, researchers have proposed numerous fast heuristic methods that provide …

Motivation Substrings of length k, commonly referred to as k-mers, play a vital role in
sequence analysis. However, k-mers are limited to exact matches between sequences …