4 hours ago by
Hi, I am doing de novo genome assembly with canu. I got two contigs, one longer contig and another shorter contig. It seems like the longer one is genome and shorter one is plasmid. When I checked the assembly after aligning the longer contig with reference genome. I see that big part of genome is aligned in different place. It is probably due to circular genome of bacteria. I want to see structural variants compared with the reference genome. I am afraid the misalignment affect on accurate estimation of structural variants. Does anyone have suggestions how to to deal with circular genome on estimating structural variants? Thanks
The aligned genome looks like the one in the following link.
