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).
Project description
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.
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