running BUSCO on unknown genomes ?

Question

[lagartija]

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,

Answer 1

[Corentin]

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.

[lagartija]

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

[Corentin]

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.

Answer 2

[kabir.deb]

Apology for the late reply, yes you can multiple files at a time, for my case I used below command line for doing so.

for i in *.fna
do
echo "${i}"
python ./run_BUSCO.py -i "${i}" -o BuScO_out_"${i}" -l lineage_odb9 -c 32 --sp fly -m genome --long -f
done;

Thanks

[GenoMax]

You are going through a set of fna files one at a time. Original poster appears to be asking if BUSCO can be run on several geomes at the same time (like program CheckM).