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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HPC version of the GMAP aligner. Runs on 16 threads on the TACC server Stampede. This aligner does spliced alignments of transcript sequences against a genome. The output is in .GFF format. 

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 -> gmap > test_inputs

Input File(s)

Use test_transcripts.fa and genome.fa from the directory above as test input, test_transcripts.fa in the sequence input and genome.fa in the reference input. The reference_indexes input is only used if you have a previously indexed genome that you want to use, instead of re-indexing the reference genome.

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 file named after the input transcripts file as output. For the test case, the output file you will find in test_output in the example_data directory is named test_transcripts.fa.out.

Tool Source for App

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