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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