The recent proliferation of next generation sequencing with short reads has enabled many
new experimental opportunities but, at the same time, has raised formidable computational …

One of the key advances in genome assembly that has led to a significant improvement in
contig lengths has been improved algorithms for utilization of paired reads (mate-pairs) …

Abstract Motivation: String and de Bruijn graphs are two graph models used by most
genome assemblers. At present, none of the existing assemblers clearly outperforms the …

Background Next-generation sequencing technologies allow genomes to be sequenced
more quickly and less expensively than ever before. However, as sequencing technology …

Background High throughput sequencing (HTS) platforms produce gigabases of short read
(< 100 bp) data per run. While these short reads are adequate for resequencing …

We have developed a new set of algorithms, collectively called “Velvet,” to manipulate de
Bruijn graphs for genomic sequence assembly. A de Bruijn graph is a compact …

Motivation: Second-generation sequencing technology makes it feasible for many
researches to obtain enough sequence reads to attempt the de novo assembly of higher …

As the advent of next-generation sequencing (NGS) technology, various de novo assembly
algorithms based on the de Bruijn graph have been developed to construct chromosome …

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 …

Motivation: Many de novo genome assemblers have been proposed recently. The basis for
most existing methods relies on the de bruijn graph: a complex graph structure that attempts …