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whole genome alignment using nucmer

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?

assembly alignment genome nucmer
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updated by harishk0201 harishk0201 • written by reza reza

2 answers

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

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written by harishk0201 harishk0201

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

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written by lieven.sterck lieven.sterck

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