[maker-devel] BUSCO

[Panos Ioannidis]

Hello Ian,

Xabier is right. You have to run BUSCO with the --long switch and then, in
the maker_opts.ctl file, you should point the augustus_species variable to
your trained species (i.e. the name you pass with the -o/-a parameter).

So, in Xabier's example your maker_opts.ctl file should contain the
following line:

augustus_species=Genus_species

Felipe, Rob, is there something else that I'm missing? Truth is that I
haven't run this recently and there might be differences in newer BUSCO
versions.

Panos


Panos Ioannidis, PhD
Postdoctoral researcher
Computational Evolutionary Genomics Group
University of Geneva

On Fri, May 13, 2016 at 2:31 AM, Xabier Vázquez Campos <xvazquezc at gmail.com>
wrote:

> Check this thread:
> https://groups.google.com/forum/#!topic/maker-devel/vp8R06VVQGQ
>
> On 26 April 2016 at 02:20, Misner, Ian (NIH/NIAID) [C] <ian.misner at nih.gov
> > wrote:
>
>> Hello,
>>
>> Are there any guidelines for using BUSCO to help train MAKER? CEGMA has
>> been discontinued but I used to use the cegma2zff.pl steps to use those
>> proteins as a training step. BUSCO seems to train Augustus but I'm not sure
>> what file to pass from BUSCO to MAKER for this to be properly utilized. I
>> didn't see anything specific about this in the archives.
>> -----
>>
>> *Ian Misner, Ph.D.*
>>
>> Computational Genomics Specialist
>>
>> Contractor, Medical Science and Computing, Inc.
>>
>> Bioinformatics and Computational Biosciences Branch (BCBB)
>>
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>>
>> 5601 Fishers Lane, Room 4A59
>>
>> Rockville, MD 20892
>>
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>>
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>>
>> Email: ian.misner at nih.gov
>>
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>> Twitter: @NIAIDBioIT
>>
>>
>>
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>
>
> --
> Xabier Vázquez-Campos, *PhD*
> *Research Associate*
> Water Research Centre
> School of Civil and Environmental Engineering
> The University of New South Wales
> Sydney NSW 2052 AUSTRALIA
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