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 …

Various graphs such as web or social networks may contain up to trillions of edges.
Compressing such datasets can accelerate graph processing by reducing the amount of I/O …

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 …

Background Long read sequencing is changing the landscape of genomic research,
especially de novo assembly. Despite the high error rate inherent to long read technologies …

Motivation New long read sequencing technologies, like PacBio SMRT and Oxford
NanoPore, can produce sequencing reads up to 50 000 bp long but with an error rate of at …

Given the popularity and elegance of k-mer-based tools, finding a space-efficient way to
represent a set of k-mers is important for improving the scalability of bioinformatics analyses …

Variation graphs, which represent genetic variation within a population, are replacing
sequences as reference genomes. Path indexes are one of the most important tools for …

The analysis of biological sequencing data has been one of the biggest applications of
string algorithms. The approaches used in many such applications are based on the …

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 …

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 …