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Pre-Requisites

  1. A CyVerse account. (Register for an CyVerse account here - user.cyverse.org)
  2. Mandatory arguments 
    1. Output folder name (name to use for the run and all temporary files (appended))
    2. Input file (genome assembly/gene set/transcript set file in FASTA format)
    3. Lineage data (Location of the BUSCO lineage data to use. You can select the BUSCO profile files for your species of interest from here : /iplant/home/shared/iplantcollaborative/the Data window under Community Data -> iplantcollaborative -> example_data /-> BUSCO.sample.datadata )
    4. Mode of analysis (genome, protein and trans. Default: genome)
  3. Optional arguments
    1. species (If your species is not in the list, selecting a closely-related species usually produces better results).
    2. e-value (Use a custom blast e-value cutoff. Default: 0.03) 
    3. long (Performs full optimization for Augustus gene finding training Default: Off

Test with sample data

The following test Test data are provided for testing BUSCO in here - /iplant/home/shared/iplantcollaborative/example_data/for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> BUSCO.sample.data. data 

Execute BUSCO with the following input data

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