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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The test data are provided for testing VIBRANT-1.0.1 is in here - /iplant/home/shared/iplantcollaborative/example_data/vibrant

Use the following inputs/outputs and parameters for VIBRANT-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. VIBRANT_log_mixed_example.log

  2. mixed_example.faa

  3. mixed_example.ffn

  4. mixed_example.gff

  5. VIBRANT_HMM_tables_parsed_mixed_example

  6. VIBRANT_HMM_tables_unformatted_mixed_example

  7. VIBRANT_figures_mixed_example

  8. VIBRANT_phages_mixed_example

  9. VIBRANT_results_mixed_example

For more detailed information about these outputs, please refer to this link - https://github.com/AnantharamanLab/VIBRANT

More information about Scythe-0.991 can be found at trim-galore manual.