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 normalize by median 

Normalize fasta or fastq reads. Eliminate reads with median k-mer abundance higher than
DESIRED_COVERAGE.

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 files as test input:

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.

  • Use these parameters within the DE app interface:
    • --ksize (kmer size, default 20. use 20 for digital normalization and 32 for partitioning)
    • --cutoff (coverage cutoff, default 20)

Output File(s)

For the test case, the output file you will find in the example_data directory is named norm-by-median_output.

Tool Source for App

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