Unfortunately, not all reference genomes will have the quality of P. falciparum. Apart from some model species (for example, humans or the common fruit fly Drosophila melanogaster) and a few others, most reference genomes could use some improvement. In this recipe, we will see how to deal with reference genomes with less quality.
In keeping with the malaria theme, here, we will use the reference genomes of two mosquitoes that are vectors of malaria: Anopheles gambiae (which is the most important vector of malaria and can be found in sub-Saharan Africa) and Anopheles atroparvus, a malaria vector in Europe (while the disease has been eradicated in Europe, this vector is still around). The An. gambiae genome is of reasonable quality. Most chromosomes have been mapped, although the Y chromosome still needs some work. There is a fairly large "unknown" chromosome, probably composed of bits X and Y chromosomes and also midgut microbiota. This...