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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Stampy-build-and-map 

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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

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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

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