From sequence mapping to genome assemblies.

The development of "next-generation" high-throughput sequencing technologies has made it possible for many labs to undertake sequencing-based research projects that were unthinkable just a few years ago. Although the scientific applications are diverse, e.g., new genome projects, gene expression analysis, genome-wide functional screens, or epigenetics-the sequence data are usually processed in one of two ways: sequence reads are either mapped to an existing reference sequence, or they are built into a new sequence ("de novo assembly"). In this chapter, we first discuss some limitations of the mapping process and how these may be overcome through local sequence assembly. We then introduce the concept of de novo assembly and describe essential assembly improvement procedures such as scaffolding, contig ordering, gap closure, error evaluation, gene annotation transfer and ab initio gene annotation. The results are high-quality draft assemblies that will facilitate informative downstream analyses.