Working with high-quality reference genomes

In this recipe, you will learn about 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 in Plasmodium falciparum, the most important parasite species that causes malaria. Reference genomes are normally made available as FASTA files.

Getting ready

Organism 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 like Plasmodium falciparum, with a 22 Mbp spread across 14 chromosomes, mitochondrion, and apicoplast, to the fruit fly with three autosomes, a mitochondrion, and X...