ERVdetective: an flexible and 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. conda method (recommend)

ervdetective has been distributed to the conda platform (https://anaconda.org/bioconda/ervdetective), and conda will automatically resolve software dependencies including blast, genometools and hmmer3. Thus, we recommend installing ervdetective by conda.

# (1) add bioconda origin
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

# (2) install ervdetective
## (i) create a separate environment for ervdetective (recommend)
conda create -n ervdetective_env python=3.7  # python >=3.6
conda activate ervdetective_env
conda install ervdetective    # or 'conda install bioconda::ervdetective'

## (ii) or installation without creating separate environment (slow)
conda install ervdetective  # or 'conda install bioconda::ervdetective'

# (3) view the help documentation
ervdetective -h

1.2. 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

Note, if ervdetective is installed by pip tool, you also need to manually install the software dependencies, please see section 2.

1.3. 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

Note, if ervdetective is installed this way, you also need to manually install the software dependencies, please see section 2.

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.

Parameter	Description
-h, --help	show this help message and exit
-i HOST	The file-path of host genome sequence, the suffix is generally *.fna, *.fas, *.fasta.
-eb EBLAST	Specify threshold of e-value for BLAST search, default: 1e-5.
-f FLANK	The length of extended flank sequence on either side of the blast hit-site, default: 15000.
-l1 MINLTR	Specify minimum length of LTR, default: 100.
-l2 MAXLTR	Specify maximum length of LTR, default: 1000.
-s LTRSIMILAR	Specify threshold(%) of the similarity of paired LTRs, default: 80.
-d1 MINDISTLTR	The minimum interval of paired-LTRs start-positions, default: 1000.
-d2 MAXDISTLTR	The maximum interval of paired-LTRs start-positions, default: 15000.
-t1 MINTSD	The minimum length for each TSD site, default: 4.
-t2 MAXTSD	The maximum length for each TSD site, default: 6.
-motif MOTIF	Specify start-motif (2 nucleotides) and end-motif (2 nucleotides), default string: TGCA.
-mis MISMOTIF	The maximum number of mismatches nucleotides in motif, default: 1.
-ed EHMMER	The threshold of e-value using for HMMER search, default: 1e-6.
-n THREAD	The the number of threads used, default: 1.
-p PREFIX	The the prefix of output file, default character: 'host'.
-o OUTPUT	The path of output folder to store all the results.
--gag GAG_LENGTH	The threshold of length of GAG protein in HMMER search, default: 250 aa.
--pro PRO_LENGTH	The threshold of length of PRO protein in HMMER search, default: 50 aa.
--rt RT_LENGTH	The threshold of length of RT protein in HMMER search, default: 150 aa.
--rh RNASEH_LENGTH	The threshold of length of RNaseH protein in HMMER search, default: 65 aa.
--int INT_LENGTH	The threshold of length of INT protein in HMMER search, default: 150 aa.
--env ENV_LENGTH	The threshold of length of ENV protein in HMMER search, default: 250 aa.

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 -n 10 -o output