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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khmer 3.0.0a1 filter-abund 

filter to remove low abundance k-mers

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 -> khmer

Input File(s)

Use these file and test input:

countgraph_19

e_coli_1000_1.fq

 e_coli_1000_2.fq

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s).

  • Use these parameters within the DE app interface:
    •  set the low abundance coverage cutoff to '2'
    • set the output filename to 'filter-abund_output.fq'

Output File(s)

Expect a fastq file named 'filter-abund_output.fq'

Tool Source for App

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