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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BWA index 0.7.4 

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Index database sequences in the FASTA format using BWA

Quick Start

  • Quick Start

    • To use BWA-0.7.12_indexer** Log in to DE and select HPC apps.
      • Under HPC apps, select BWA-0.7.12_indexer.
      • Define the path to the reference genome in FASTA format under the Inputs tab.
      • Enter the prefix term and choose algorithm for constructing BWT index under the Parameters tab. 
      • Indexed files will be generated and written to files named using the prefix term. 

Test Data

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Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> bwa-mem -> inputs

Input File(s)

Use BAgenomeRay41.fa from the directory above as test input.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

 

  • Default parameters only, no further configuration needed.

Output File(s)

Expect a files named after the input file as output. For the test case, the output file you will find in the example_data directory is named BAgenomeRay41.fa.64.amb, BAgenomeRay41.fa.64.ann, BAgenomeRay41.fa.64.bwt, BAgenomeRay41.fa.64.pac, and BAgenomeRay41.fa.64.sa.

Tool Source for App

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