Mercurial > repos > petr-novak > dante_ltr

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"planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
author petr-novak
date Tue, 08 Mar 2022 13:24:33 +0000
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1 # dante_ltr
2
3 Tool for identification of complete LTR retrotransposons based on analysis of protein
4 domains identified by DANTE tool.
5
6 ## Installation:
7
8 ```shell
9 conda create -n dante_ltr -c bioconda -c conda-forge -c petrnovak dante_ltr
10 ```
11 ## Usage
12
13 ```shell
14 Usage: ./extract_putative_ltr.R COMMAND [OPTIONS]
15
16
17 Options:
18 -g GFF3, --gff3=GFF3
19 gff3 with dante results
20
21 -s REFERENCE_SEQUENCE, --reference_sequence=REFERENCE_SEQUENCE
22 reference sequence as fasta
23
24 -o OUTPUT, --output=OUTPUT
25 output file path and prefix
26
27 -c NUMBER, --cpu=NUMBER
28 Number of cpu to use [default 5]
29
30 -h, --help
31 Show this help message and exit
32 ```
33
34 ## Example
35 ```shell
36 mkdir -p tmp
37 ./extract_putative_ltr.R -g test_data/sample_DANTE.gff3 -s test_data/sample_genome.fasta -o tmp/ltr_annotation
38 ```
39
40 ## Output files
41
42
43 ### Output of script `extract_putative_ltr.R`:
44
45
46 - `prefix.gff3` - annotation of all identified elements
47 - `prefix_DL.fasta` - elements with protein **d**omains and **L**TR
48 - `prefix_DLTP.fasta` - elements with **d**omains, **L**TR, **T**SD and **P**BS
49 - `prefix_DLP.fasta` - elements with **d**omains, **L**TR and **P**BS
50 - `prefix_DLT.fasta` - elements with **d**omains, **L**TR, **T**SD
51 - `prefix_statistics.csv` - number of elements in individual categories