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annotate README.md @ 12:ff01d4263391 draft

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"planemo upload commit 414119ad7c44562d2e956b765e97ca113bc35b2b-dirty"
author petr-novak
date Thu, 21 Jul 2022 08:23:15 +0000
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1 # DANTE_LTR
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3 Tool for identifying complete LTR retrotransposons based on analysis of protein domains identified with the [DANTE tool](https://github.com/kavonrtep/dante). Both DANTE and DANTE_LTR are available on [Galaxy server](ttps://repeatexplorer-elixir.cerit-sc.cz/).
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5 ## Principle of DANTE _LTR
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6 Complete retrotransposons are identified as clusters of protein domains recognized by the DANTE tool. The domains in the clusters must be assigned to a single retrotransposon lineage by DANTE. In addition, the orientation and order of the protein domains, as well as the distances between them, must conform to the characteristics of elements from REXXdb database [Neumann et al. (2019)](https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-018-0144-1).
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7 In the next step, the 5' and 3' regions of the putative retrotransposon are examined for the presence of 5' and 3' long terminal repeats. If 5'- and 3'-long terminal repeats are detected, detection of target site duplication (TSD) and primer binding site (PSB) is performed. The detected LTR retrotranspsons are classified into 5 categories:
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8 - Elements with protein domains, 5'LTR, 3'LTR, TSD and PBS - rank **DLTP**.
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9 - Elements with protein domains, 5'LTR, 3'LTR, and PBS (TSD was not found) Rank **DLP**
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10 - Elements with protein domains, 5' LTR, 3'LTR, TSD (PBS was not found) - rank **DTL**
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11 - Elements with protein domains, 5'LTR and 3'LTR (PBS and TDS were not found) - rank **DL**
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12 - Elements as clusters of protein domains with the same classification, no LTRs - rank **D**.
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14 ![dante_ltr_workflow.png](dante_ltr_workflow.png)
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17 ## Installation:
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19 ```shell
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20 conda create -n dante_ltr -c bioconda -c conda-forge -c petrnovak dante_ltr
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21 ```
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23 ## Input data
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24 One input is a reference sequence in fasta fromat. The second input is an annotation of the reference genome using the tool DANTE in GFF3 format. For better results, use the unfiltered full output of the DANTE pipeline.
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27 ## Usage
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29 ### Detection of complete LTR retrotransposons
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31 ```shell
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32 Usage: ./detect_putative_ltr.R COMMAND [OPTIONS]
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35 Options:
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36 -g GFF3, --gff3=GFF3
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37 gff3 with dante results
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39 -s REFERENCE_SEQUENCE, --reference_sequence=REFERENCE_SEQUENCE
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40 reference sequence as fasta
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42 -o OUTPUT, --output=OUTPUT
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43 output file path and prefix
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45 -c NUMBER, --cpu=NUMBER
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46 Number of cpu to use [default 5]
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47
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48 -M NUMBER, --max_missing_domains=NUMBER
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49 Maximum number of missing domains is retrotransposon [default 0]
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50
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51 -L NUMBER, --min_relative_length=NUMBER
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52 Minimum relative length of protein domain to be considered for retrostransposon detection [default 0.6]
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53 -h, --help
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54 Show this help message and exit
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56 ```
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57
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58 #### Example:
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59
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60 ```shell
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61 mkdir -p tmp
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62 ./detect_putative_ltr.R -g test_data/sample_DANTE.gff3 -s test_data/sample_genome.fasta -o tmp/ltr_annotation
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63 ```
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64
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65 #### Files in the output of `extract_putative_ltr.R`:
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67 - `prefix.gff3` - annotation of all identified elements
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68 - `prefix_D.fasta` - partial elements with protein **d**omains
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69 - `prefix_DL.fasta` - elements with protein **d**omains and **L**TR
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70 - `prefix_DLTP.fasta` - elements with **d**omains, **L**TR, **T**SD and **P**BS
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71 - `prefix_DLP.fasta` - elements with **d**omains, **L**TR and **P**BS
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72 - `prefix_DLT.fasta` - elements with **d**omains, **L**TR, **T**SD
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73 - `prefix_statistics.csv` - number of elements in individual categories
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75 For large genomes, you can your `detect_putative_ltr_wrapper.py`. This script will split input fasta to smaller chunks and run `detect_putative_ltr.R` on each chunk to limit memory usage. Output will be merged after all chunks are processed.
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76
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77 ```shell
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78 usage: detect_putative_ltr_wrapper.py [-h] -g GFF3 -s REFERENCE_SEQUENCE -o
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79 OUTPUT [-c CPU] [-M MAX_MISSING_DOMAINS]
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80 [-L MIN_RELATIVE_LENGTH]
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81 [-S MAX_CHUNK_SIZE]
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83 detect_putative_ltr_wrapper.py is a wrapper for
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84 detect_putative_ltr.R
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85
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86 optional arguments:
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87 -h, --help show this help message and exit
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88 -g GFF3, --gff3 GFF3 gff3 file
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89 -s REFERENCE_SEQUENCE, --reference_sequence REFERENCE_SEQUENCE
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90 reference sequence as fasta file
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91 -o OUTPUT, --output OUTPUT
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92 output file path and prefix
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93 -c CPU, --cpu CPU number of CPUs
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94 -M MAX_MISSING_DOMAINS, --max_missing_domains MAX_MISSING_DOMAINS
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95 -L MIN_RELATIVE_LENGTH, --min_relative_length MIN_RELATIVE_LENGTH
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96 Minimum relative length of protein domain to be considered
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97 for retrostransposon detection
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98 -S MAX_CHUNK_SIZE, --max_chunk_size MAX_CHUNK_SIZE
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99 If size of reference sequence is greater than this value,
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100 reference is analyzed in chunks of this size. This is
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101 just approximate value - sequences which are longer
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102 are are not split, default is 100000000
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103 ```
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105 ### Validation of LTR retrotransposons detected un previous step:
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106
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107 ```shell
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108 ./clean_ltr.R --help
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109 Usage: ./clean_ltr.R COMMAND [OPTIONS]
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110
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111
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112 Options:
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113 -g GFF3, --gff3=GFF3
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114 gff3 with LTR Transposable elements
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115
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116 -s REFERENCE_SEQUENCE, --reference_sequence=REFERENCE_SEQUENCE
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117 reference sequence as fasta
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118
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119 -o OUTPUT, --output=OUTPUT
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120 output file prefix
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121
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122 -c NUMBER, --cpu=NUMBER
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123 Number of cpu to use [default 5]
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124
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125 -h, --help
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126 Show this help message and exit
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127 ```
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128
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129 This script check for potentially chimeric elements and removes them from GFF3 file.
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130
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131 #### Example
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132 ```shell
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133 ./clean_ltr.R -g test_data/sample_DANTE_LTR_annotation.gff3 -s test_data/sample_genome.fasta -o tmp/ltr_annotation_clean
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134 ```
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135