8.1. Introduction

Genomic analyses take several forms. At one level, any study that draws inferences for protein-coding genes or other genetic traits in the context of their neighbors on chromosomes is ‘genomic’. More recently, genomic studies are those that use massive DNA sequencing strategies to describe and piece together entire sections of the targeted genome, without using PCR or other selective techniques to target specific short regions. Ultimately, genomic studies hope to assemble chromosome-length stretches of an organism’s genetic blueprint, and then annotate or describe the functionality of specific regions within chromosomes. The field of genomics is driven by technological advances, including huge cost reductions for the sequencing of samples and advances in both statistical methods and computational resources for analysing the obligatory large datasets.  Current estimates indicate that entire pipelines (sets of routines needed for an output analysis) are viable for only six months before becoming obsolete. One helpful review of modern techniques is given by Desai et al. (2012) and there are numerous advances and tutorials available via the forums Seqanswers.com and the GALAXY wiki (http://wiki.galaxyproject.org/FrontPage). Researchers are advised to consult these sources while planning genomic, transcriptomic, and metagenomic projects, as the standards and possible analyses are improving constantly.