The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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  1. A CyVerse account. (Register for a CyVerse account here - user.cyverse.org.)

  2. Input

    1. Input fasta file

  3. Parameters
  4. Format of input {prot,nucl} [default="nucl"]
  5. Number of parallel VIBRANT runs, each occupies 1 CPU [default=1, max of 1 CPU per scaffold]
  6. Length in basepairs to limit input sequences. Default is 1000, can increase but not decrease

  7. Number of ORFs per scaffold to limit input sequences. Default is 4, can increase but not decrease

  8. virome. Use this setting if the dataset is known to be comprised mainly of viruses. More sensitive to viruses, less sensitive to false identifications [default=off]
  9. no_plot. suppress the generation of summary plots [default=off]

Test/sample data:


The test data are provided for testing VIBRANTFLIP-1.0 .1 is in here - /iplant/home/shared/iplantcollaborative/example_data/vibrant 

Use the following inputs/outputs and parameters for VIBRANTFLIP-1.0.1

  1. Input 

    1. Input fasta file: /iplant/home/shared/iplantcollaborative/example_data/vibrant/example_data/mixed_example.fasta

  2. Parameters
    1. Format of input: Nucleotide
    2. Number of parallel VIBRANT runs: 1 
    3. Length in basepairs to limit input sequences: 1000 

    4. Number of ORFs per scaffold to limit input sequences: 4 

Leave the rest of the two as defaults

Output Reports:

After successful completion of the run, expect the following files as output:

  1.  

For more detailed information about these outputs, please refer to this link - 

 

 

 

 

 

 

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