whole genome alignment using nucmer

Question

[reza]

hi

i aligned two whole genome using nucmer with this simple command

nucmer reference_genome.fasta query_genome.fasta

then three outputs files were created: out.delta, out.coordinates, out.tiling

Now, is there any way to know how percent of reference genome, covered by query genome?

Answer 1

[harishk0201]

You can use dnadiff from the MUMmer suite actually. It will generate a .report file where all the details are present.

Answer 2

[lieven.sterck]

Not as such I think, you will have to post-process one of those output files (the out.coordinates if I remember well)

[lieven.sterck]

there you go :), I upvoted harishk0201 answer myself