khmer 3.0.0a1 extract paired reads

split remaining paired and single-end reads with khmer strip-and-split-for-assembly

Quick Start

• To use khmer 3.0.0a1 extract paired reads, 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 paired reads
  • name a separate output file for single reads

Output File(s)

Expect a fastq file name extract_paired_output.fq as output. There are no single reads in the input file. If there were they would be output into a second output file. 

Tool Source for App

• https://github.com/dib-lab/khmer