From Sequence Mapping to Genome Assemblies [chapter]

Thomas D. Otto
2014 Msphere  
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 scientifi c 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
more » ... into a new sequence ("de novo assembly"). In this chapter, we fi rst 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.
doi:10.1007/978-1-4939-1438-8_2 pmid:25388106 fatcat:dobmztvzlbctbf6yjz24cshake