Bioinformatic procedures for host genomics can be grouped in two main tasks, the generation of the reference genome and the resequencing of the genome. The first one aims at creating a (often single) reference genome sequence for a species, a breed or a population, which is then used to generate genomic profiles for multiple individuals. Reference genomes generation requires a considerably higher sequencing effort than resequencing, and the use of multiple sequencing technologies (long-read, Hi-C, etc.) is often needed to resolve the structural complexities of most eukaryotic organisms. Genome resequencing, in contrast, usually relies on short-read sequencing, which provide sufficient information for calling nucleotide variarions.
Overviews of both procedures are shown in the following chapters: