I just assembled a plasmid using Illumina 2x250 PE. I am pretty confident that the assembly is fine.
I check by mapping the raw data to the assembly. In general I have a very high coverage (sometimes more than 1000x). Also I have very few unmapped pairs.
But I have some regions where the coverage drops to 10-20 fold coverage. This looks concerning, but I still think my assembly is fine because:
1. I this areas I also see barely unmapped pairs
2. I did not see more missmatches from the reads to the assembly sequence as in other regions
Now my questions:
1. What are the properties of sequences where Illumina gives a lower coverage? Any paper? Or a SW to check?
2. How else can I check if my assembly is fine in this low coverage areas?