Question: Assessing collapsed assembly ?
gravatar for Picasa
8 months ago by
Picasa590 wrote:

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.

paralogue collapsing assembly • 171 views
ADD COMMENTlink modified 8 months ago by colindaven2.6k • written 8 months ago by Picasa590
gravatar for colindaven
8 months ago by
Hannover Medical School
colindaven2.6k wrote:

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.

ADD COMMENTlink written 8 months ago by colindaven2.6k
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