How to clean up a genome assembly

Slimane is assembling the genome of the fungus Botrytis cinerea which usually infects a wide range of plant hosts such as legumes, wine grapes and other fruits.

He first made a preliminary assembly, and then mapped all the reads from the DNA sequencing libraries to that assembly. He used the BTK Pipeline (which you will learn about later) to create a preliminary blobplot.

Figure 1

Slimane was able to use the BTK viewer to identify the contigs that he thought were contaminants, and he removed them step by step.

In the next article you will see how he removed the contaminants step by step, and how he saved a list of the contigs/sequences belonging to the fungus of interest