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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Bowtie2-2.2.4 Bowtie2-Build indexer and aligner

This tutorial covers two TACC-HPC apps in the DE: 1. bowtie2-2.2.4_indexer for creating an index of your reference genome. 2. bowtie2-2.2.4_aligner for aligning reads to your indexed genome.

Quick Start

  • To use Bowtie2-2.2.4-indexer
    • Log in to DE and select HPC apps.
    • Under HPC apps, select Bowtie2-2.2.4-indexer.
    • Define the path to the reference genome in FASTA format.
    • Enter the prefix term. 
    • Indexed files will be generated and written to files named using the prefix term. 
  • To use Bowtie2-2.2.4-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.
    • Enter prefix for output files.
    • Define path to single, paired, or long (local alignment) reads file. 
    • Aligned files will be written to files, in SAM format, named with output file prefix, followed by 1.sam for single reads, 2.sam for paired reads, and 3.sam for long reads. 
  • Resources: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#the-bowtie2-aligner

Test Data for bowtie2-2.2.4_indexer

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> bowtie2-2.2.4_indexer.

Input File(s)

Use lambda_virus.fa from the directory above as test input for bowtie2-2.2.4_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 - bt_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 "bt_test_1".

Test Data for bowtie2-2.2.4_aligner

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> bowtie2-2.2.4_aligner.

Input File(s)

Define path to indexed genome files: Output directory with indexed files from bowtie2-2.2.4-indexer.

Define path to single reads file: reads_1.fq

Define path to paired reads file: reads_2.fq

Define path to local alignment reads file: longreads.fq

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:
    • Enter prefix for indexed files - bt_test_1
    • Enter prefix for output SAM files - testalign1

Output File(s)

Expect a SAM file named after the prefix as output. For the test case, the output file you will find in the example_data directory will begin with the prefix "testalign1".

Tool Source for App

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