[maker-devel] BUSCO

Fri May 13 10:25:56 MDT 2016

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

On May 13, 2016, at 3:28 AM, Robert Waterhouse <robert.waterhouse at gmail.com<mailto:robert.waterhouse at gmail.com>> wrote:

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
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A maturing understanding of the composition of the insect gene repertoire COIS 2015<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.sciencedirect.com_science_article_pii_S2214574515000073&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=jK3HLznqS7mlwXNI4FHO3K_o5EX29RgO9ccngyj7Dzg&s=bQEtPdLzzK-aA_CU1jUsGJSpOVJj1L8KQPqEy3Y3ryk&e=>
BUSCO: assessing genome assembly and annotation completeness Bioinformatics 2015<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioinformatics.oxfordjournals.org_content_early_2015_06_27_bioinformatics.btv351.full&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=jK3HLznqS7mlwXNI4FHO3K_o5EX29RgO9ccngyj7Dzg&s=QUFAzNyvgTS2NMA6NvMruQWvuH7WVrkJbdqiwBD5QvA&e=>

On 13 May 2016 at 09:56, Panos Ioannidis <panos.ioannidis at gmail.com<mailto:panos.ioannidis at gmail.com>> wrote:
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<mailto:xvazquezc at gmail.com>> wrote:
Check this thread:
https://groups.google.com/forum/#!topic/maker-devel/vp8R06VVQGQ<https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_forum_-23-21topic_maker-2Ddevel_vp8R06VVQGQ&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=jK3HLznqS7mlwXNI4FHO3K_o5EX29RgO9ccngyj7Dzg&s=LOPsrMMxPBDmfBDJTBpsLGpYd7_pecEb7rxNXO-oOnw&e=>

On 26 April 2016 at 02:20, Misner, Ian (NIH/NIAID) [C] <ian.misner at nih.gov<mailto: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<https://urldefense.proofpoint.com/v2/url?u=http-3A__cegma2zff.pl&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=jK3HLznqS7mlwXNI4FHO3K_o5EX29RgO9ccngyj7Dzg&s=R1NsitSMN4RwzwYuaNjszxmyBogW6wSOa8NWl4Sny_k&e=> 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
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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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