Introduction

This software generates rarefaction data from Kraken output. The software organizes reads into subsamples and reports the number of taxa present within each subsample for all principal classification ranks. The output of this software is in csv format.

Release

Krakefaction 0.2.0

Installation

This software is compatible with Python 2.7 and Python 3. The following may check your Python version:

python --version

The user must insure the following requirements are met:

• Python 2.7 or Python 3
• virtualenv
• pip

The software will be installed using pip into its own Python virtual environment. The following will install the software locally into the source directory and will not require security privileges:

krakefaction/INSTALL.sh

Alternatively, you may specify an install location, PREFIX, such as /usr/local/. The software will create the directories PREFIX/lib and PREFIX/bin. This may require security privileges:

krakefaction/INSTALL.sh PREFIX

Running Krakefaction

Krakefaction's command line arguments can be found by running:

krakefaction --help

A simple example of running Krakefaction:

krakefaction -u untranslated.tab -t translated.tab -o output.csv

Contact

Eric Marinier: eric.marinier@canada.ca

Legal

Copyright Government of Canada 2018

Written by: Eric Marinier, National Microbiology Laboratory, Public Health Agency of Canada

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this work except in compliance with the License. You may obtain a copy of the License at:

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.