khmer 3.0.0a1 load into counting
split remaining paired and single-end reads with khmer strip-and-split-for-assembly
- To use khmer 3.0.0a1 load into counting, import your data in filtered paired end fastq format.
- Resources: http://khmer.readthedocs.io/en/v2.1.1/user/scripts.html#scripts-read-handling
Use a paired end, filtered fastq file as test input.
Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.
- Use these parameters within the DE app interface:
- name output file for countgraph file–
- set the k-mer size to 19
Expect a fastq file named countgraph_19 as output.
Tool Source for App