whole genome alignment using nucmer
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2.1 years ago
reza ▴ 250

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 • 1.2k views
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2.0 years ago
harishk0201 ▴ 110

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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2.1 years ago

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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there you go :), I upvoted harishk0201 answer myself

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