deviaTE 0.3.8

Analysis and visualization of mobile genetic element composition

deviaTE

deviaTE is a python tool for the analysis and visualization of mobile genetic element sequences. It is available for Unix and Linux systems.

Installation

Using Conda

The recommended way of using deviaTE is in a conda virtual environment. This way, all dependencies should be resolved.

Create a new conda virtual environment, and install deviaTE:

conda create deviaTE -c r -c defaults -c conda-forge -c bioconda -c w-l -n deviaTE_env

this command loads all required anaconda channels (r, defaults, conda-forge, bioconda, w-l) and names the environment deviaTE_env

The environment can then be activated, and deviaTE with all necessary dependencies can be used inside the environment:

source activate deviaTE_env

After using deviaTE, the environment can be exited using:

source deactivate

Using pip

DeviaTE can also be installed with the pip python package manager. However, this does not take care of all dependencies. The following tools need to be set up manually beforehand:

• python 3.6+
• pip for python3 (https://pip.pypa.io/en/stable/installing/)
• samtools (tested with version 1.6 and 1.9)
• bwa (tested with version 0.7.17)
• R (tested with version 3.4.3)
  • required R packages are installed automatically upon first usage

samtools and bwa need to be in your $PATH

DeviaTE can then be installed with

pip3 install deviaTE

Uninstallation

conda environment:

conda env remove -n deviaTE_env

pip package:

pip3 uninstall deviaTE

Usage manual, walkthroughs and reference

A manual and a walkthrough with examples using publicly available data can be found here:

• Manual
• Walkthrough

A paper describing deviaTE is available here:

• https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13030

@article{weilguny2019,
 author = {Weilguny, Lukas and Kofler, Robert},
 title = {{DeviaTE}: {Assembly-free} analysis and visualization of mobile genetic element composition},
 journal = {Molecular Ecology Resources},
 volume = {Accepted Author Manuscript},
 year= {2019},
 doi = {10.1111/1755-0998.13030}
}

Bugs, issues, questions, suggestions ...

If you find any problems, have questions or ideas for further improvement please use the issue tracker on this repository, thanks!

License

deviaTE is licensed under the GPLv3 License