Entering edit mode
16 months ago
rthapa
▴
60
Hi, I am using MUMmer plot to compare between a de novo assembly with reference genome. The percent identity between two genomes is more than 99% but when I plot the two genomes with MUMmer plot, the plot (https://ibb.co/q08xsZw) doesn't look like that. Does anyone have any idea? Thanks
Have you tried to reverse complement one of the sequences before trying this again? I don't recollect if MUMmer tries that.
No, I did't try the reverse complement. Do you have any suggestion on tools that we can use for getting reverse complement? The alignment looks like https://ibb.co/cL6ydYr with mauve.
You can use
reformat.sh
from BBMap suite to do the reverse complement.It looks like the reverse complement is better to visualize. It seems like there are two inversions in the assembled genome https://ibb.co/k5MqYqZ.
Those blue segments represent inversions and translocations (which are apparent in your
mauve
plots too).Thank you. But when I check the mummer results for structural variation, there are four inversion in the assembly compared to reference genome. I wonder why mummer plot is showing only two inversions.
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