An introduction to the algorithms and tools used to reconstruct genome sequences from shotgun sequencing data and to annotate the resulting sequence. Course includes theoretical underpinnings of core assembly paradigms and the practical use of paradigms; approaches for scaffolding the reconstructed sequences along chromosomes using mate-pair and other types of information; and validating sequence assemblers output. The course will discuss approaches for interpreting sequence annotations in the context of a reconstructed genome, focusing on genome browsers and other visualization and analytical tools and approaches for interpreting gene synteny information. A particular focus will be on the impact of repetitive sequences on the quality of genome assemblies and ability to effectively analyze gene synteny and to conduct comparative genomic analyses.