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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GSNAP 121212

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An HPC version of the GSNAP splice alignment application.

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 -> gsnap.

Input File(s)

Use the ecSeqs directory from the directory above as test input. Use the E coli genome (in the gsnap directory) as a reference. 

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 Ecoli as the index name. Otherwise use defaults completely.

Output File(s)

Expect a .sam file for each of the input files as output. For the test case, the output files will each be named "inputfilename".sam.

Tool Source for App

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