khmer 3.0.0a1 normalize by median
- de-confluence
- amcooksey (Unlicensed)
- Susan Miller
Owned by de-confluence
khmer 3.0.0a1 normalize by medianÂ
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. Â
- Resources:Â https://khmer.readthedocs.org/en/latest/guide.html
Test Data
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.