MUMmer overall identity & output
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18 months ago
yp19 ▴ 70

Hi guys! I want to use nucmer to assess how similar two species' assemblies are to one another. I used the command like this:

nucmer sp1_scaffolds.fa sp2_scaffolds.fa --coords

and in the output I get a series of alignment records with the following columns

[S1]  [E1]  |  [S2]  [E2]  |  [LEN 1]  [LEN 2]  |  [% IDY]  | [TAGS]

I have two questions about this:

  1. Does anyone know if nucmer produces one value to represent how similar the species are to one another? (for example, an overall identity score)
  2. Is this output table filtered in anyway? I don't see every single scaffold in the TAGS column (perhaps there is a minimum identity filter that nucmer applies?). Currently my %IDY values range from 80-100%.

Thank you for any thoughts.

MUMmer nucmer species • 383 views
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