Working with high-quality reference genomes

In this recipe, you will learn a few general techniques to manipulate reference genomes. As an illustrative example, we will study the GC content (the fraction of the genome that is based on Guanine-Cytosine). Reference genomes are normally made available as FASTA files.

Getting ready

Genomes come in widely different sizes, ranging from viruses such as HIV (which is 9.7 kbp) to bacteria such as E. coli, to protozoans such as Plasmodium falciparum (the most important parasite species causing malaria) with its 14 chromosomes, mitochondrion, and apicoplast, to the fruit fly with three autosomes, a mitochondrion, and X/Y sex chromosomes, to humans with its three Gbp pairs spread across 22 autosomes, X/Y chromosomes, and mitochondria, all the way up to Paris japonica, a plant with 150 Gbp of genome. Along the way, you have different ploidy and different sex chromosome organizations.

Tip

As you can see, different organisms have very different genome sizes...