Quality control by mapping

In this part of the tutorial we will look at the assemblies by mapping the contigs of our first assembly to the reference genome using Minimap2, samtools and GenomeView.

Map the data and inspect with GenomeView

Your task is, to map the WGS assembly to the Wuhan reference, create a sorted and indexed bam file and view the results in GenomeView.

The mapping result file (sorted bam) should be named:

~/workdir/mappings/assembly_wgs_vs_wuhan.sorted.bam

You already did that a few times, so we are quite confident, you can do that without help. If not - check out the next page.