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1 # Changelog
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2
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3
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4 ## v0.3.5
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5 Nov 22 2019
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6
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7 - better reporting when filtering of abundant satellite is used
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8 - number of changes in names of output files - file names are now more informative. Changes include:
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9
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10 | old file name | new file name |
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11 |--------------------------------------------------------------------------|----------------------------------------------------------------------|
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12 | TR_consensus_rank_1_.fasta | TAREAN_consensus_rank_1.fasta |
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13 | TR_consensus_rank_2_.fasta | TAREAN_consensus_rank_2.fasta |
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14 | TR_consensus_rank_3_.fasta | TAREAN_consensus_rank_3.fasta |
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15 | TR_consensus_rank_4_.fasta | TAREAN_consensus_rank_4.fasta |
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16 | sequences/sequences.fasta | reads/reads.fasta |
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17 | clustering/clusters/dir_CL0001/reads.fas.CL1.aln.info.minRD5_sort-GR | clustering/clusters/dir_CL0001/contigs.info.minRD5_sort-GR.fasta |
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18 | clustering/clusters/dir_CL0001/reads.fas.CL1.aln.info.minRD5_sort-length | clustering/clusters/dir_CL0001/contigs.info.minRD5_sort-length.fasta |
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19 | clustering/clusters/dir_CL0001/reads.fas.CL1.aln.info.minRD5 | clustering/clusters/dir_CL0001/contigs.info.minRD5_sort-RD.fasta |
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20 | clustering/clusters/dir_CL0001/reads.fas.CL1.aln.profile | clustering/clusters/dir_CL0001/contigs.profile |
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21 | clustering/clusters/dir_CL0001/reads.fas.CL1.aln.info | clustering/clusters/dir_CL0001/contigs.info.fasta |
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22 | clustering/clusters/dir_CL0001/reads.fas.CL1.ace | clustering/clusters/dir_CL0001/contigs.ace |
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23 | clustering/clusters/dir_CL0001/reads.fas.CL1.contigs.qual | clustering/clusters/dir_CL0001/contigs.qual |
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24 | clustering/clusters/dir_CL0001/reads.fas.CL1.aln | clustering/clusters/dir_CL0001/contigs.aln |
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25 | clustering/clusters/dir_CL0001/reads.fas.CL1.contigs | clustering/clusters/dir_CL0001/contigs.fasta |
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26 | clustering/clusters/dir_CL0001/reads.fas.CL1.info | clustering/clusters/dir_CL0001/assembly.info |
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27 | clustering/clusters/dir_CL0001/reads.fas.CL1.singlets | clustering/clusters/dir_CL0001/singlets.fasta |
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28 | clustering/clusters/dir_CL0001/reads.fas.CL1.contigs.links | clustering/clusters/dir_CL0001/contigs.links |
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29 | clustering/clusters/dir_CL0001/reads_oriented.fas | clustering/clusters/dir_CL0001/reads_selection_oriented.fasta |
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30 | clustering/clusters/dir_CL0001/CL1_directed_graph.RData. | clustering/clusters/dir_CL0001/graph_layout_directed.RData |
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31 | clustering/clusters/dir_CL0001/CL1_tmb.png | clustering/clusters/dir_CL0001/graph_layout_tmb.png |
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32 | clustering/clusters/dir_CL0001/CL1.png | clustering/clusters/dir_CL0001/graph_layout.png |
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33 | clustering/clusters/dir_CL0001/CL1.GL | clustering/clusters/dir_CL0001/graph_layout.GL |
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34 | clustering/clusters/dir_CL0001/blast.csv | clustering/clusters/dir_CL0001/hitsort_part.csv |
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35
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36 ## v0.3.4
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37 Oct 31 2019
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38
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39 - Classification of superclusters improved, classification now uses information about LTR/PBS for classification of Class_I elements
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40
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41
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42 ## v0.3.2
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43 Oct 9 2019
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44
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45 - Graphical reporting of comparative analysis added
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46
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47 ## v0.3.1
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48 Jan 9 2019
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49
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50 - Improved detection of low complexity repeats and satellites with shorter monomer
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51
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52 ## v0.3.0
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53 Oct 25 2018
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54
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55 - For back-compatibility, it is possible to select protein database version
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56 - Databases of protein domains went public
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57
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58 ## v0.2.10
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59 Oct 24 2018
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60
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61 - Protein database for Viridiplantae updated
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62
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63 ## v0.2.9
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64 Jan 3 2018
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65
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66 - read depth for contigs is calculated
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67 - contigs are also sorted based on genome representation
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68
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69 ## v0.2.8
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70 Dec 18 2017
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71
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72 - by default assembly is done on clusters with size at least 5 reads
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73 - preset option of Illumina, Illumina short and Oxford Nanopore
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74 - option for analyzing Metazoa/ Viridiplantae added
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75 - protein databases can be obtained **using fetch_databases.sh** script (password required)
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76
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77 ## v0.2.7
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78 Dec 05 2017
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79
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80 - improved DNA database - protein domain were masked not to interfere with protein domain database
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81 - another bug fix in parallelization and assembly
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82 - alternative to blastx added - DIAMOND program can be used instead
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83
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84 ## v0.2.6
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85 Nov 14 2017
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86
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87 - Improved classification of superclusters
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88 - tables in HTML reports improved
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89 - assembly is performed on low confidence satellite sequences
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90 - assembly optimized, bug fix in parallelization
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91
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92 ## v0.2.5
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93 Sep 1 2017
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94
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95 + More options added to _galaxy interface_ of TAREAN and RepeatExplorer2:
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96 - automatic satellite filtering
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97 - cluster size threshold setting
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98 - keep original sequence names option
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99 + Pipeline tests added
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100
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101 ## v0.2.4
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102 Aug 10 2017
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103
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104 - Filtering of abundant satellite sequences
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105 - Improved (more sensitive) search of protein domains
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106 - bug fix in parallelization
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107 - SHORT_ILLUMINA option added, this enable to analyze shorter reads (50nt) - command line only
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108 - OXFORD_NANOPORE option added (experimental feature, command line only)
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109
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110 ## v0.2.3
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111 Jun 9 2017
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112
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113 - some changes in standalone TAREAN
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114
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115 ## v0.2.2
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116
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117 - improved visualization of comparative analysis
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118
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119 ## v0.2.1
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120
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121 - log file is automatically copied to output and is part of archive(in galaxy)
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122
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123 ## v0.2.0
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124
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125 + Improved HTML output
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126 + Updated documentation
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127 + Full clustering analysis - RepeatExplorer2
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128 + New features:
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129 - Cap3 assembly added
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130 - Comparative analysis
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131 - LTR detection from contigs
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132 - Custom database option
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133 - Bugfix in excessive CPU usage
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134 - Detection of TE protein domains
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135
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136 ## v0.1.1
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137
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138 + New features:
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139 - Cluster merging
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140 - Scan of clusters against DNA database (detection of rDNA, plastid, mitochondrial and contaminants)
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141
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142 ## v0.1.0
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143
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144
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145
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