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 …

The recent advances in sequencing technologies enable the assembly of individual
genomes to the quality of the reference genome. How to integrate multiple genomes from …

Background De novo genome assembly relies on two kinds of graphs: de Bruijn graphs and
overlap graphs. Overlap graphs are the basis for the Celera assembler, while de Bruijn …

Memory consumption of de Bruijn graphs is often prohibitive. Most de Bruijn graph-based
assemblers reduce the complexity by compacting paths into single vertices, but this is …

We propose a new succinct de Bruijn graph representation. If the de Bruijn graph of k-mers
in a DNA sequence of length N has m edges, it can be represented in 4 m+ o (m) bits. This is …

Compacted de Bruijn graphs are one of the most fundamental data structures in
computational genomics. Colored compacted de Bruijn graphs are a variant built on a …

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

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 …

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 …

Motivation The construction of the compacted de Bruijn graph from collections of reference
genomes is a task of increasing interest in genomic analyses. These graphs are increasingly …