MUMmer plot visualization

Question

[rthapa]

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

[GenoMax]

Have you tried to reverse complement one of the sequences before trying this again? I don't recollect if MUMmer tries that.

[rthapa]

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.

[GenoMax]

You can use reformat.sh from BBMap suite to do the reverse complement.

reformat.sh in=seq.fa out=rc.fa rcomp=t

[rthapa]

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.

Is the red bar present in the right corner duplicated region in the reference genome? Do you have any idea if I need to get reverse complement to call the structural variants with Mummer or I can just use the de novo assembly?

[GenoMax]

Those blue segments represent inversions and translocations (which are apparent in your mauve plots too).

[rthapa]

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.

tig00000001 INV 228534  226344  -2189
tig00000001 GAP 745271  742507  -2763   -232    -2531
tig00000001 GAP 765321  764991  -329    -151    -178
tig00000001 INV 872150  866517  -5632
tig00000001 GAP 1199745 1199745 1   -47 48
tig00000001 GAP 1900829 1900827 -1  -13978  13977
tig00000001 GAP 2499469 2498978 -490    -336    -154
tig00000001 DUP 2561758 2562745 988
tig00000001 BRK 2562746 2563397 652
tig00000001 DUP 2563398 2563566 169
tig00000001 BRK 2563567 2563570 4
tig00000001 INV 2769150 2763519 -5630
tig00000001 INV 3375024 3372831 -2192
tig00000001 JMP 3688215 3688214 0

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