The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

The box below searches only this space.
To search the entire iPlant wiki, enter your query in the box at the upper right.






Skip to end of metadata
Go to start of metadata

BWA 0.7.4 Divergent species

Community rating: ?????

Index and map short reads to a reference sequence with BWA (Default settings optimised for mapping 50bp reads to a divergent species)

Quick Start

Test Data


Input File(s)

Use the fastq file above as test input.

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.

  • Default parameters only, no further configuration needed

Output File(s)

Expect a SAM file as output. For the test case, the output file you will find as an example is as follows:

Tool Source for App

  • No labels