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Assessing collapsed assembly ?

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.

assembly paralogue collapsing
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updated by colindaven colindaven • written by Picasa Picasa

1 answer

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.

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written by colindaven colindaven

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