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

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

• http://khmer.readthedocs.io/en/v2.1.1/user/scripts.html#scripts-read-handling