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



Community rating: ?????

Stampy is a package for the mapping of next gen sequencing reads onto a reference genome. Stampy excels in the mapping of reads containing sequence variation relative to the reference, especially indels.

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 -> Stampy

Input File(s)

Use the test_1.fastq file from the directory above as test input with the genome sequence provided, NC_010473.fa.

Parameters Used in App

  • Default parameters only, except set the output file name to stampyout.sam


Output File(s)

Expect a SAM file named stampyout.sam as output in the test case.

Tool Source for App

  • No labels