High-throughput sequencing data sets are usually deposited in public repositories (eg, the
European Nucleotide Archive) to ensure reproducibility. As the amount of data has reached …

Processing large data sets has become an essential part of computational genomics.
Greatly increased availability of sequence data from multiple sources has fueled …

k-mer-based methods are widely used in bioinformatics for various types of sequence
comparisons. However, a single mutation will mutate k consecutive k-mers and make most k …

The de Bruijn graph is a key data structure in modern computational genomics, and
construction of its compacted variant resides upstream of many genomic analyses. As the …

Sequencing data are rapidly accumulating in public repositories. Making this resource
accessible for interactive analysis at scale requires efficient approaches for its storage and …

When indexing large collections of short-read sequencing data, a common operation that
has now been implemented in several tools (Sequence Bloom Trees and variants, BIGSI) is …

Abstract de Bruijn graphs play an essential role in bioinformatics, yet they lack a universal
scalable representation. Here, we introduce simplitigs as a compact, efficient, and scalable …

Motivation A plethora of methods and applications share the fundamental need to associate
information to words for high-throughput sequence analysis. Doing so for billions of k-mers …

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 …

Motivation Bloom filters are a popular data structure that allows rapid searches in large
sequence datasets. So far, all tools work with nucleotide sequences; however, protein …