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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

ddRAGE (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

For parameter visualization:

  • bokeh

Installation

We recommend the installation using conda:

$ conda create -n ddrage -c bioconda ddrage
$ source activate ddrage

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

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

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

Usage

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

$ ddrage

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

$ ddrage -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.

Project details


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Filename, size & hash SHA256 hash help File type Python version Upload date
ddrage-1.4.0-py3-none-any.whl (235.1 kB) Copy SHA256 hash SHA256 Wheel py3 Oct 18, 2017
ddrage-1.4.0.tar.gz (227.3 kB) Copy SHA256 hash SHA256 Source None Oct 18, 2017

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