Question: running BUSCO on unknown genomes ?
0
gravatar for lagartija
4 weeks ago by
lagartija50
lagartija50 wrote:

Hi,

I'm trying to assess my genome completeness and possible contamination with busco. Is it possible to run it several files at the same time ? Is it also possible not to use a reference species when orfing with augustus while running BUSCO ? I am trying to find an equivalent to checkm but for eukaryotes. It seems less feasible but I would like to know if you had any suggestions.

Thank you very much, Cheers,

assembly • 136 views
ADD COMMENTlink modified 4 weeks ago by Corentin260 • written 4 weeks ago by lagartija50
1
gravatar for Corentin
4 weeks ago by
Corentin260
Corentin260 wrote:

Hi,

I do not think it is possible to use more than one genome.

You do not have to use a reference species (from the user manual, https://gitlab.com/ezlab/busco/raw/master/BUSCO_v3_userguide.pdf):

(NB: without specifying a particular species, Augustus species parameters will be selected according to the predefined defaults)

So just select the relevant set for your genome and run BUSCO, of course the results will be less accurate than if you specify a species.

I am not sure how you want to assess the contamination from the BUSCO results. There are other tools for this (like Kraken https://ccb.jhu.edu/software/kraken/), which one to use is dependant on your data.

ADD COMMENTlink written 4 weeks ago by Corentin260

Thank you for your answer. I think the default parameter is the fruit fly. Can I avoid orfing by augustus somehow ?

ADD REPLYlink written 4 weeks ago by lagartija50

I do not think you can skip Augustus.

The default parameter depends on the lineage you choose (cf the table on page 14 of the user guide). https://gitlab.com/ezlab/busco/raw/master/BUSCO_v3_userguide.pdf

If your species is not in Augustus' list, you can choose a closely related species and it should still give you informative results.

ADD REPLYlink written 4 weeks ago by Corentin260
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