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 …

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 …

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 …

Sequence-level searches on large collections of RNA sequencing experiments, such as the
NCBI Sequence Read Archive (SRA), would enable one to ask many questions about the …

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 …

Motivation Indexing reference sequences for search—both individual genomes and
collections of genomes—is an important building block for many sequence analysis tasks …

Motivation Almost all de novo short-read genome and transcriptome assemblers start by
building a representation of the de Bruijn Graph of the reads they are given as input. Even …

Abstract Motivation The de Bruijn graph is fundamental to the analysis of next generation
sequencing data and so, as datasets of DNA reads grow rapidly, it becomes more important …

The de Bruijn graph, a fundamental data structure to represent and organize genome
sequence, plays important roles in various kinds of sequence analysis tasks. With the rapid …

The monotone minimal perfect hash function (MMPHF) problem is the following indexing
problem. Given a set S={s ı,…, sn} of n distinct keys from a universe U of size u, create a data …