[maker-devel] BUSCO

[Robert Waterhouse]

I would guess that the main 'advantage' of using BUSCO to train Augustus is
that one will probably run BUSCO on one's genome anyway before starting
MAKER, so there will already be a useful set of trained parameters ready to
use. I guess the 'advantage' of using the Augustus webtraining service is
that one could give it much more starting data (if indeed this is
available, e.g. cDNAs). Indeed if there was enough time and it made a
substantial difference one might even use the BUSCO gene model output as
the 'Training gene structure file' for Augustus webtraining service. I
don't believe that anyone has done a comparison on how different the
trained parameters end up being.

Rob


  \\      Dr Robert Waterhouse
O0o--    SIB maître assistant
  ""    www.rmwaterhouse.org

A maturing understanding of the composition of the insect gene repertoire COIS
2015 <http://www.sciencedirect.com/science/article/pii/S2214574515000073>
BUSCO: assessing genome assembly and annotation completeness Bioinformatics
2015
<http://bioinformatics.oxfordjournals.org/content/early/2015/06/27/bioinformatics.btv351.full>

On 13 May 2016 at 12:14, Dolze, Florian <fdolze at students.uni-mainz.de>
wrote:

>
> On a somewhat related note, is there an advantage of using BUSCO to train
> Augustus instead of the provided Augustus webtraining service? Does anybody
> know how those 2 compare?
>
>
>
> Am 13.05.2016 um 09:56 schrieb 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>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>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.
>>>
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>>>
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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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