Introduction

In this section, we improve our understanding of de Bruijn graphs by studying many ‘non-tranditional’ applications. Most de Bruijn graph-based assemblers for next-generation sequences were originally written to perform de novo genome assembly from single-ended Illumina reads. After that effort became successful, researchers started incorporating other technologies (Illumina paired end reads and mate pairs, Sanger reads, 454 reads, ABI-SOLiD, PacBio, etc.), and ventured to solve other biological problems (transcriptome assembly, metagenome assembly, etc.). We say ‘non-traditional’ in quotes, because by now most of the mentioned applications have become mainstream in this rapidly advancing field. The following discussions are divided into two parts – (a) de Bruijn graphs for different sequencing technologies (considered in this section), and (b) de Bruijn graphs to address various biological questions (next section). To be clear, the main purpose of these two sections is to let you have more practice with de Bruijn graph concepts by thinking through many applications, and not to promote it as the only way to solve those assembly problems.