Assessing collapsed assembly ?

Question

[Picasa]

Hi all,

I have 2 different genomes and I am looking to assess if one assembly is more collapsed than the other one (example: if paralogues are collapsed in one assembly more than the other).

Do you have any idea how can I do this ? I am also open to papers that have reported this problem too.

Thanks for your help.

Answer 1

[colindaven]

You can try calling ORFs / genes in each and doing bidirectional blast to produce a CSV output, eg with proteinortho.

A: Reciprocal blast hit

Alternatively, you could look at BUSCO which would be the more standard approach.