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BWA-0.7.4 non-model species


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Index and map short reads to a reference sequence with BWA

App Name

BWA Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. This instance of BWA works with paired-end sequencing reads.

Quick Start

Test Data


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

Input File(s)


Input File(s)

Use 10K_SRR192294_1.fastq (2.4M) and 10K_SRR192294_2.fastq (2.4M) as test data. Import from URL to get the data into your Discovery Environment account.

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 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.


  • Use these parameters within the DE app interface:
  • parameter name - value/setting
  • parameter name - value/settingSelect a reference genome from the list - Brachypodium distachyon (line Bd21) v1
  • All other parameters remain in their default state

Output File(s)

Expect a text SAM file named after the input files as output. For the test case, the output file you will find in the example_data directory is named 10K_SRR192294_1.fastq-10K_SRR192294_2.fastq.sam (4.8M)

Tool Source for App