assemblies with very high duplicated busco scores

[tothuhien]

Hi, I have 2 assemblies with very high duplicated busco scores (78% and 92%). The histograms of them are like this:

and this

Do you think it’s normal to have histograms like this with very high duplicated busco score? And I’m not sure how to pick the cut-off values for the next step. Thank you very much for your help.

Best regards,

Hien

[Michael Roach]

Hi Hien,

The first histogram looks like you have a mostly phased assembly. Run the cov step with -l 5 -m 100 -h 200 and it should work fine.

The second histogram looks like it’s completely phased, or the peaks are overlapping. either way you should just flag all the contigs; the same settings will work fine: -l 5 -m 100 -h 200

If you do have almost completely phased genomes, it would be good to submit both the primary contigs and haplotigs as a diploid assembly!

All the best,

Mike

[tothuhien]

Thank you very much for your prompt response. I will try that. I had those assemblies by just running canu, so I didn’t know that they are already mostly phased.

Thanks,

Hien