ddRAGE — ddRAD Data Generator
| Main Authors: | Henning Timm, Sven Rahmann |
|---|---|
| Format: | info software Journal |
| Bahasa: | eng |
| Terbitan: |
, 2020
|
| Subjects: | |
| Online Access: |
https://zenodo.org/record/4390216 |
Daftar Isi:
- 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 /ddrage$ 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 or in the documentation folder (see index.html).