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

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

• https://github.com/dib-lab/khmer