Dealing with low-quality genome references

Unfortunately, not all reference genomes will have the quality of Plasmodium 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 learn how to deal with reference genomes of lower quality.

Getting ready

In keeping with the malaria theme, 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 Anopheles 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 of X and Y chromosomes, as well...