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

HTProcess_Kmergenie-1.0

Community rating: ?????

Part of the HTProcess group of applications. Runs Kmergenie on all the reads in a library and analyzes the kmer population.

Quick Start

  • To use HTProcess_Kmergenie-1.0, import your data in the form of the HTProcess_Reads directory output from the HTProcess_prepare-directories-and-run-fastqc app.
  • Resources: http://kmergenie.bx.psu.edu/

Test Data

Icon

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> htprocess1 -> HTProcess _prepare_directories-and-run_fastqc

Input File(s)

Use the directory HTProcess_Reads in 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.

Set the lower kmer limit to 21 and the upper limit to 31, with an increment of 10. Diploid is set to false and 2 passes are run.

Output File(s)

Expect the files found in Community Data -> iplantcollaborative -> example_data -> htprocess1 -HTProcess_kmergenie. Click on Kmergenie_report.html to open the report from Kmergenie in the DE.

Tool Source for App

  • No labels