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BWA index 0.7.

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Index database sequences in the FASTA format using BWA

Quick Start

• Quick Start

  • To
  use BWA index
  • use BWA-0.7.
  4, import your data in ___ format.Resources: http://replace.with.URL.for.tool.documentation.from.the.tool.source.org
  • 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

Input File(s)

Use TerriblyIncomprehensible.txt and HorriblyWritten.txt from BAgenome41.fa from the directory above as test input.

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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.

Use either the "Default parameters..." section OR fill in the "Use these parameters..." section. Delete the unused section and the OR. Then, delete this note. 

• Default parameters only, no further configuration needed.

OR

• Use these parameters within the DE app interface:
• parameter name - value/setting
parameter name - value/setting

Output File(s)

Expect a text file files named after the input files as file as output. For the test case, the output file you will find in the example_data directory is named BeautifulProse.txt.

Tool Source for App

• http://replacebio-bwa.with.URL.for.tool.orgsourceforge.net/