Assessment of the coverage

This post is just some description and reflection on the coverage of the data, since it is good to know if there are any “weak spots” of the assembly.

I downloaded and installed Geneious Prime with a 14 days trial license. I aligned the paired end reads to the assembled contig. Then I used the built in tool for calculation of coverage in Geneious Prime (with default settings). The output showed regions of high coverage and regions of low coverage. As seen in the image below the high coverage region (yellow part) includes the region of the terminal repeats that was found with PhageTerm (and now confirmed in Geneious Prime). The regions of low coverage (red part) are just at the ends of the assembly, where it would be expected to be a lower reads due to lower quality of the reads. Overall the coverage seems to be good with no gaps.

The assembled contig with annotation of the terminal repeats (orange part) and coverage. Yellow part for high coverage and red for low coverage.