The amount of biological sequencing data available in public repositories is growing
exponentially, forming an invaluable biomedical research resource. Yet, making all this …

The colored compacted de Bruijn graph (c-dBG) has become a fundamental tool used
across several areas of genomics and pangenomics. For example, it has been widely …

The decrease in sequencing expenses has facilitated the creation of reference genomes
and proteomes for an expanding array of organisms. Nevertheless, no established …

Motivation Exponential growth in sequencing databases has motivated scalable De Bruijn
graph-based (DBG) indexing for searching these data, using annotations to label nodes with …

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 …

Metagenomics, the study of the genome sequences of diverse organisms in a common
environment, has led to significant advances in many fields. Since the species present in a …

The amount of data stored in genomic sequence databases is growing exponentially, far
exceeding traditional indexing strategies' processing capabilities. Many recent indexing …

In this paper, we introduce the Conway-Bromage-Lyndon (CBL) structure, a compressed,
dynamic and exact method for representing k-mer sets. Originating from Conway and …

Efficient pangenome indexes are promising tools for many applications, including rapid
classification of nanopore sequencing reads. Recently, a compressed-index data structure …

We describe lossless compressed data structures for the colored de Bruijn graph (or, c-
dBG). Given a collection of reference sequences, a c-dBG can be essentially regarded as a …