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Close gaps in scaffolds created with Soapdenovo.
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> gap closer > input
Use soapoutputdirectory from the directory 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.
The exact scaffold name in your assembly directory must be entered.
For the test data, the maximum read length is 101. The rest is left default.
Expect a text file named after the input scaffold as output -- "_gapcloser.fa" will be added.