[maker-devel] BUSCO

[Misner, Ian (NIH/NIAID) [C]]

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)

NIH/NIAID/OD/OSMO/OCICB

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[Xabier Vázquez Campos]

Check this thread:
https://groups.google.com/forum/#!topic/maker-devel/vp8R06VVQGQ

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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

[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

[Dolze, Florian]

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?

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[Robert Waterhouse]

I think in the Augustus 'species' directory there should be a new folder named according to your BUSCO run, and in that folder should be the trained parameters for your new species, so from MAKER I guess you can point to these trained parameters.

Rob

  \\      Dr Robert Waterhouse

O0o--    SIB maître assistant

  ""    www.rmwaterhouse.org

A maturing understanding of the composition of the insect gene repertoire COIS 2015

BUSCO: assessing genome assembly and annotation completeness Bioinformatics 2015

[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

BUSCO: assessing genome assembly and annotation completeness Bioinformatics 2015

[Fields, Christopher J]

Our group have mainly used the BUSCO model in the ‘bootstrap’ run for MAKER, then retrain Augustus and SNAP using a filtered data set from that run for new rounds of MAKER.

Also, one personal observation: we have found some genome assemblies where BUSCO performs poorly compared to CEGMA (e.g. BUSCO reports poor overall percent of SCO present, while CEGMA reports much higher numbers).  We’re still delving into this, but in those cases we avoid using the BUSCO model for obvious reasons.

chris