12 Host genomics (HG) data processing

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: