The exponential increase in sequencing data calls for conceptual and computational
advances to extract useful biological insights. One such advance, minimizers, allows for …

Long-read sequencing has recently transformed metagenomics, enhancing strain-level
pathogen characterization, enabling accurate and complete metagenome-assembled …

High-quality genome assemblies and sophisticated algorithms have increased sensitivity for
a wide range of variant types, and breakpoint accuracy for structural variants (SVs,≥ 50 bp) …

Seed-chain-extend with k-mer seeds is a powerful heuristic technique for sequence
alignment used by modern sequence aligners. Although effective in practice for both runtime …

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

Co-linear chaining is a widely used technique in sequence alignment tools that follow seed-
filter-extend methodology. It is a mathematically rigorous approach to combine short exact …

Background As an important forage in arid and semi-arid regions, Agropyron cristatum
provides livestock with exceptionally high nutritional value. Additionally, A. cristatum exhibits …

Motivation A common method for analyzing genomic repeats is to produce a sequence
similarity matrix visualized via a dot plot. Innovative approaches such as StainedGlass have …

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

Background Sequence alignment lies at the heart of genome sequence annotation. While
the BLAST suite of alignment tools has long held an important role in alignment-based …