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 0.7.12 indexer aligner and mem

This tutorial covers three TACC-HPC apps in the DE:

1. BWA-0.7.12_indexer for creating an index of your reference genome.

2. BWA-0.7.12_aligner for aligning reads to your indexed genome.

3. BWA-0.7.12_mem for ######.

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. 
  • To use BWA-0.7.12_aligner
    • Log in to DE and select HPC apps.
    • Under HPC apps, select Bowtie2-2.2.4-aligner.
    • Define the path to the directory of indexed genome files.
    • Enter the prefix term used to create the index files.
    • Define path to the FASTQ file.
    • Enter name for output file. This term will be used with suffix ".sai".
    • Define parameters under Parameters tab. 
  • Resources: http://bio-bwa.sourceforge.net/bwa.shtml

Test Data for bwa-0.7.12_indexer

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> bwa-0.7.12.

Input File(s)

Use 10K_SRR192294_1.fastq.unmapped.fa from the directory above as test input for bwa-0.7.12_indexer.

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.

  • Use these parameters within the DE app interface:
    • prefix - bwa_test_1

Output File(s)

Expect a text file named after the prefix as output. For the test case, the output files you will find in the example_data directory will begin with the prefix "bwa_test_1".

Test Data for bwa-0.7.12_aligner

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> bwa-0.7.12.

Input File(s)

Define path to indexed genome files: Output directory with indexed files from bwa-0.7.12-indexer.

Define path to FASTQ file: 10K_SRR192294_1.fastq

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.

Output File(s)

Expect a file named after the prefix as output with "sai" as suffix. 

Tool Source for App

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