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The CyVerse App Store is currently being restructured, and apps are being moved to an HPC environment. During this transition, users may occasionally be unable to locate or use apps that are listed in our tutorials. In many cases, these apps can be located by searching them using the search bar at the top of the Apps window in the DE. To increase the chance for search success, try not searching the entire app name and version number but only the portion that refers to the app's function or origin (e.g. 'SOAPdenovo' instead of 'SOAPdenovo-Trans 1.01').

Also, as part of the 2.8 app categorization, a number of apps were deprecated and are no longer available, and there is no longer an Archive category. You can search for a suitable replacement in the List of Applications in this window, or search on an app name or tool used for an app in the Apps window search field. If you need an app reinstated, please contact

titleTutorial under review

For an introduction to using the DE, see Using the Discovery Environment.

Please work through the tutorial and add your comments on the bottom of this page, or email comments to Thank you.

Rationale and background

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. You can use BWA mem to align 70bp-1Mbp query sequences with the BWA-MEM algorithm, and to index and map Illumina reads (70-100bp) to a reference sequence.


  1. A CyVerse account (Register for a CyVerse account at

  2. An up-to-date Java-enabled web browser. (Firefox recommended. If you wish to work with your own large datasets and upload them using iCommands, Chrome is not suitable due to its issues in utilizing 64-bit Java.)

Test/sample data

This tutorial uses the test data that is stored in the Data Store at Community Data > iplantcollaborative > example_data > bwa          

  1. Use 10K_SRR192294_1.fastq for Left_Read file and 10K_SRR192294_2.fastq (2.4M) for Right_Read file
  2. Select a reference genome from the list - Brachypodium distachyon (line Bd21) v1
  3. All other parameters remain in their default state


Expect a SAM file named after the input files as output. For the test case, the output file is 10K_SRR192294_1.fastq-10K_SRR192294_2.fastq.sam (4.8M)

Tool Source for App