The last decade has witnessed an explosion in the amount of available biological sequence
data, due to the rapid progress of high-throughput sequencing projects. However, the …

Motivation: As the quantity of data per sequencing experiment increases, the challenges of
fragment assembly are becoming increasingly computational. The de Bruijn graph is a …

Motivation: Error correction is critical to the success of next-generation sequencing
applications, such as resequencing and de novo genome sequencing. It is especially …

De novo whole genome assembly reconstructs genomic sequence from short, overlap**,
and potentially erroneous fragments called reads. We study optimized parallelization of the …

De novo whole genome assembly reconstructs genomic sequences from short, overlap**,
and potentially erroneous DNA segments and is one of the most important computations in …

Background Next-generation sequencing technologies have given rise to the explosive
increase in DNA sequencing throughput, and have promoted the recent development of de …

Combinatorial techniques have become essential tools across the landscape of
computational science, and some of the combinatorial ideas undergirding these tools are …

Metagenome assembly is the process of transforming a set of short, overlap**, and
potentially erroneous DNA segments from environmental samples into the accurate …

We introduce a new concept of a subgraph class called a superbubble for analyzing
assembly graphs, and propose an efficient algorithm for detecting it. Most assembly …

From the Foreword:" The authors of the chapters in this book are the pioneers who will
explore the exascale frontier. The path forward will not be easy... These authors, along with …