Normalize fasta or fastq reads. Eliminate reads with median k-mer abundance higher than
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> khmer
Use these files as test input:
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)
For the test case, the output file you will find in the example_data directory is named norm-by-median_output.