ddrage 1.2.2

Simulator for ddRADseq (double digest restriction site associdated DNA squencing) datasets. Generates reads (FASTQ format) that can be analyzed and validated using a ground truth file (YAML).

RAGE (ddRAD Data Generator) is a software to simulate double digest restriction site associated DNA sequencing reads. The generated data sets can be used to test ddRAD analysis tools and validate their results.

The documentation, including a tutorial, can be found here. The code is hosted on bitbucket, PyPI, and bioconda.

System Requirements

• python >= 3.5

• numba

• numpy

• matplotlib

• pyyaml

• scipy

For the docs:

• sphinx

• sphinx_rtd_theme

For parameter visualization:

• bokeh

Installation

We recommend the installation using conda:

$ conda create -c bioconda -n rage  python rage
$ source activate rage

Alternatively, you can download the source code from bitbucket and install it using the setup script:

$ git clone https://bitbucket.org/genomeinformatics/rage.git
$ cd rage
/rage$ python setup.py install

In this case you have to install the requirements listed above.

Usage

To simulate a ddRAD data set, call rage from the command line:

$ rage

you can specify parameters to change data set parameters such as number of individuals (-n), nr of loci (-l), and coverage (--coverage):

$ rage -n 6 -l 10000 --coverage 30

This creates a data set with reads from 6 individuals at 10000 loci with an expected coverage of 30.

A more detailed tutorial can be found on readthedocs.