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

• To use khmer 3.0.0a1 normalize by median, import your data in fastq format.  
• Resources: https://khmer.readthedocs.org/en/latest/guide.html

Test Data

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

• https://github.com/ged-lab/khmer