# 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](https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/) (version >=2.9.0+), has to contain ```makeblastdb``` and ```tblastn```.
+ [genometools](http://genometools.org) (version >=1.6.1), has to contain ```ltrharvest```.
+ [hmmer](http://hmmer.org/) (version >=3.0), has to contain ```hmmpress``` and ```hmmscan```.
<b>Note</b>, 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 -o output
```
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"description": "# ERVdetective: an efficient pipeline for identification and annotation of endogenous retroviruses (ERVs)\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n## 1. Download and install\r\n\r\nervdetective is a command-line-interface program developed based on ```Python 3```, and you can download and install the ervdetective in a variety of ways.\r\n\r\n### 1.1. pip method\r\n\r\nervdetective has been distributed to the standard library of ```PyPI``` (https://pypi.org/project/ervdetective/), and can be easily installed by the tool ```pip```.\r\n\r\nFirstly, download ```Python3``` (https://www.python.org/), and install ```Python3``` and ```pip``` tool, then,\r\n\r\n```\r\npip install ervdetective\r\nervdetective -h\r\n```\r\n\r\n### 1.2. Or local installation\r\n\r\nIn addition, ervdetective can also be installed manually using the file using the file ```setup.py```. \r\n\r\nFirstly, download this repository, then, run:\r\n```\r\npython setup.py install\r\nervdetective -h\r\n```\r\n\r\n### 1.3. Or run the source code directly\r\n\r\nyou can also directly run the source code of ervdetective without installation. First, download this repository, then, install the required python environment of ervdetective:\r\n\r\n```\r\npip install -r requirements.txt -i https://pypi.tuna.tsinghua.edu.cn/simple\r\n```\r\n\r\nfinally, run ervdetective using the file ```main.py```. Please view the help documentation by ```python main.py -h```.\r\n\r\n\r\n## 2. Software dependencies\r\n\r\nThe running of ```ervdetective``` relies on these softwares:\r\n\r\n+ [blast](https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/) (version >=2.9.0+), has to contain ```makeblastdb``` and ```tblastn```.\r\n\r\n+ [genometools](http://genometools.org) (version >=1.6.1), has to contain ```ltrharvest```. \r\n\r\n+ [hmmer](http://hmmer.org/) (version >=3.0), has to contain ```hmmpress``` and ```hmmscan```. \r\n\r\n\r\n<b>Note</b>, 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.\r\n\r\n\r\n## 3. Getting help\r\n\r\nThe help documentation can be get by entering ```ervdetective -h``` or ```ervdetective --help```.\r\n\r\n| Parameter | Description |\r\n| --- | --- |\r\n|-h, --help | show this help message and exit|\r\n|-i HOST | The file-path of host genome sequence, the suffix is generally *.fna, *.fas, *.fasta.|\r\n|-eb EBLAST | Specify threshold of e-value for BLAST search, default: 1e-5.|\r\n|-f FLANK | The length of extended flank sequence on either side of the blast hit-site, default: 15000.|\r\n|-l1 MINLTR | Specify minimum length of LTR, default: 100.|\r\n|-l2 MAXLTR | Specify maximum length of LTR, default: 1000.|\r\n|-s LTRSIMILAR | Specify threshold(%) of the similarity of paired LTRs, default: 80.|\r\n|-d1 MINDISTLTR | The minimum interval of paired-LTRs start-positions, default: 1000.|\r\n|-d2 MAXDISTLTR | The maximum interval of paired-LTRs start-positions, default: 15000.|\r\n|-t1 MINTSD | The minimum length for each TSD site, default: 4.|\r\n|-t2 MAXTSD | The maximum length for each TSD site, default: 6.|\r\n|-motif MOTIF | Specify start-motif (2 nucleotides) and end-motif (2 nucleotides), default string: TGCA.|\r\n|-mis MISMOTIF | The maximum number of mismatches nucleotides in motif, default: 1.|\r\n|-ed EHMMER | The threshold of e-value using for HMMER search, default: 1e-6.|\r\n|-n THREAD | The the number of threads used, default: 1.|\r\n|-p PREFIX | The the prefix of output file, default character: 'host'.|\r\n|-o OUTPUT | The path of output folder to store all the results.|\r\n|--gag GAG_LENGTH | The threshold of length of GAG protein in HMMER search, default: 250 aa.|\r\n|--pro PRO_LENGTH | The threshold of length of PRO protein in HMMER search, default: 50 aa.|\r\n|--rt RT_LENGTH | The threshold of length of RT protein in HMMER search, default: 150 aa.|\r\n|--rh RNASEH_LENGTH | The threshold of length of RNaseH protein in HMMER search, default: 65 aa.|\r\n|--int INT_LENGTH | The threshold of length of INT protein in HMMER search, default: 150 aa.|\r\n|--env ENV_LENGTH | The threshold of length of ENV protein in HMMER search, default: 250 aa.|\r\n\r\n\r\n## 4. Example of usage\r\n\r\nThe bat Myotis myotis (GCA_004026985.1) , and its genome data was downloaded from https://www.ncbi.nlm.nih.gov/datasets/taxonomy/51298/\r\n\r\nThen, run:\r\n\r\n```\r\nervdetective -i GCA_004026985.1_MyoMyo_v1_BIUU_genomic.fna -p myotis_myotis -o output\r\n```\r\n",
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