annotate README.md @ 0:7b0bbe7477c4 draft

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# dante_ltr

Tool for identification of complete LTR retrotransposons based on analysis of protein
domains identified by DANTE tool.

## Installation:

```shell
conda create -n dante_ltr -c bioconda -c conda-forge -c petrnovak dante_ltr
```
## Usage

```shell
Usage: ./extract_putative_ltr.R COMMAND [OPTIONS]


Options:
        -g GFF3, --gff3=GFF3
                gff3 with dante results

        -s REFERENCE_SEQUENCE, --reference_sequence=REFERENCE_SEQUENCE
                reference sequence as fasta

        -o OUTPUT, --output=OUTPUT
                output file path and prefix

        -c NUMBER, --cpu=NUMBER
                Number of cpu to use [default 5]

        -h, --help
                Show this help message and exit
```

## Example
```shell
mkdir -p tmp
./extract_putative_ltr.R -g test_data/sample_DANTE.gff3 -s test_data/sample_genome.fasta -o tmp/ltr_annotation
```

## Output files


### Output of script `extract_putative_ltr.R`:


- `prefix.gff3` - annotation of all identified elements
- `prefix_DL.fasta` - elements with protein **d**omains and **L**TR
- `prefix_DLTP.fasta` - elements with **d**omains, **L**TR, **T**SD and **P**BS
- `prefix_DLP.fasta` - elements with **d**omains, **L**TR and **P**BS
- `prefix_DLT.fasta` - elements with **d**omains, **L**TR, **T**SD 
- `prefix_statistics.csv` - number of elements in individual categories