ERVdetective: an efficient pipeline for identification and annotation of endogenous retroviruses (ERVs)

1. Download and install

ervdetective is a command-line-interface program developed based on Python 3, and you can download and install the ervdetective in a variety of ways.

1.1. pip method

ervdetective has been distributed to the standard library of PyPI (https://pypi.org/project/ervdetective/), and can be easily installed by the tool pip.

Firstly, download Python3 (https://www.python.org/), and install Python3 and pip tool, then,

pip install ervdetective
ervdetective -h

1.2. Or local installation

In addition, ervdetective can also be installed manually using the file using the file setup.py.

Firstly, download this repository, then, run:

python setup.py install
ervdetective -h

1.3. Or run the source code directly

you can also directly run the source code of ervdetective without installation. First, download this repository, then, install the required python environment of ervdetective:

pip install -r requirements.txt -i https://pypi.tuna.tsinghua.edu.cn/simple

finally, run ervdetective using the file main.py. Please view the help documentation by python main.py -h.

2. Software dependencies

The running of ervdetective relies on these softwares:

• blast (version >=2.9.0+), has to contain makeblastdb and tblastn.

• genometools (version >=1.6.1), has to contain ltrharvest.

• hmmer (version >=3.0), has to contain hmmpress and hmmscan.

Note, these dependencies need to be installed and added to environment variables of system (or user) beforehand, because ervdetective call them from the environment variables directly.

3. Getting help

The help documentation can be get by entering ervdetective -h or ervdetective --help.

4. Example of usage

The bat Myotis myotis (GCA_004026985.1) , and its genome data was downloaded from https://www.ncbi.nlm.nih.gov/datasets/taxonomy/51298/

Then, run:

ervdetective -i GCA_004026985.1_MyoMyo_v1_BIUU_genomic.fna -p myotis_myotis -o output