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:
- Does anyone know if nucmer produces one value to represent how similar the species are to one another? (for example, an overall identity score)
- 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.