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
2. Software dependencies
The running of ervdetective relies on these softwares:
-
blast (version >=2.9.0+), has to contain
makeblastdbandtblastn. -
genometools (version >=1.6.1), has to contain
ltrharvest. -
hmmer (version >=3.0), has to contain
hmmpressandhmmscan.
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
1 maintainer
Metadata
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Release files for ervdetective 1.0.9
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| ervdetective-1.0.9.tar.gz | 998.2 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| ervdetective-1.0.9-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 2.0 MB
Release files / ervdetective-1.0.9.tar.gz
| Download URL | ervdetective-1.0.9.tar.gz |
|---|---|
| Size | 998.2 kB |
| Tags | Source |
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