khmer 3.0.0a1 filter-abund
khmer 3.0.0a1 filter-abund
filter to remove low abundance k-mers
Quick Start
- To use khmer 3.0.0a1 filter-abund, import your data in fastq format.
- Resources: http://khmer.readthedocs.io/en/v2.1.1/user/scripts.html#scripts-read-handling
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 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