Videos on : (a) the Burrows-Wheeler Transform (BWT), (b) the FM Index, which uses the BWT to construct a full-text index, (c) Wheeler graphs, (d) r-index, an...

We introduce Mapping-friendly Sequence Reduction (MSR) sketches, a sketching method for high-fidelity (HiFi) long reads, and Alice, an assembler that operates directly on these sketches. MSR produces ...

Abstract Summary In this article, we introduce the Conway–Bromage–Lyndon (CBL) structure, a compressed, dynamic and exact method for representing k-mer sets. Originating from Conway and Bromage’s concept, CBL innovatively employs the smallest cyclic rotations of k-mers, akin to Lyndon words, to leverage lexicographic redundancies. In order to support dynamic operations and set operations, we propose a dynamic bit vector structure that draws a parallel with Elias-Fano’s scheme. This structure is encapsulated in a Rust library, demonstrating a balanced blend of construction efficiency, cache locality, and compression. Our findings suggest that CBL outperforms existing dynamic k-mer set methods. Unique to this work, CBL stands out as the only known exact k-mer structure offering in-place set operations. Its different combined abilities position it as a flexible Swiss knife structure for k-mer set management. Availability and implementation https://github.com/imartayan/CBL.

Using sequencing and haplotype-resolved assembly of 65 diverse human genomes, complex regions including the major histocompatibility complex and centromeres are analysed.

We introduce FAMSA2, an algorithm that produces high-accuracy multiple protein sequence alignments with unprecedented speed. Across structural, phylogenetic, and functional benchmarks, FAMSA2 matches ...