[maker-devel] BUSCO

[Xabier Vázquez Campos]

Having installed Augustus, BUSCO will generate the training files in the
Augustus species folder. Afterwards you only need to indicate the species
profile in the Maker config file as usual.

BUSCO developers say that the long run produces a better profile and should
be used if you run the program to train Augustus. This is the command I used

python3 BUSCO_v1.1b1.py -f -c 8 --long -o Genus_species -in
> /PATH/TO/ASSEMBLY/contigs.fa -l /PATH/TO/PROFILE/fungi -m genome
>


On 26 April 2016 at 13:04, Barry Moore <bmoore at genetics.utah.edu> wrote:

> I’m posting this message to the mailing list on behalf of Ian Misner.
> Ian, sorry your message and subscription request hasn’t gone through.  The
> ISP that supports all of our mailing lists including maker is having issues
> with the mailman software that they can’t seem to resolve, so we currently
> can’t approve held messages or add new subscribers.  We’re in the process
> of working out a new mailing list option.  Thanks for you patience!
>
> Begin forwarded message:
>
> 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, *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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