khmer 3.0.0a1 load into counting
khmer 3.0.0a1 load into counting
split remaining paired and single-end reads with khmer strip-and-split-for-assembly
Quick Start
- 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
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 a paired end, filtered fastq file as test input.
e_coli_1-2.fq
Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) 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
Output File(s)
Expect a fastq file named countgraph_19 as output.
Tool Source for App