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author petrn
date Fri, 20 Dec 2019 14:17:59 +0000
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7:c56807be3b72 8:3bc73f5dc785
1 # Changelog
2
3
4 ## v0.3.5
5 Nov 22 2019
6
7 - better reporting when filtering of abundant satellite is used
8 - number of changes in names of output files - file names are now more informative. Changes include:
9
10 | old file name | new file name |
11 |--------------------------------------------------------------------------|----------------------------------------------------------------------|
12 | TR_consensus_rank_1_.fasta | TAREAN_consensus_rank_1.fasta |
13 | TR_consensus_rank_2_.fasta | TAREAN_consensus_rank_2.fasta |
14 | TR_consensus_rank_3_.fasta | TAREAN_consensus_rank_3.fasta |
15 | TR_consensus_rank_4_.fasta | TAREAN_consensus_rank_4.fasta |
16 | sequences/sequences.fasta | reads/reads.fasta |
17 | clustering/clusters/dir_CL0001/reads.fas.CL1.aln.info.minRD5_sort-GR | clustering/clusters/dir_CL0001/contigs.info.minRD5_sort-GR.fasta |
18 | clustering/clusters/dir_CL0001/reads.fas.CL1.aln.info.minRD5_sort-length | clustering/clusters/dir_CL0001/contigs.info.minRD5_sort-length.fasta |
19 | clustering/clusters/dir_CL0001/reads.fas.CL1.aln.info.minRD5 | clustering/clusters/dir_CL0001/contigs.info.minRD5_sort-RD.fasta |
20 | clustering/clusters/dir_CL0001/reads.fas.CL1.aln.profile | clustering/clusters/dir_CL0001/contigs.profile |
21 | clustering/clusters/dir_CL0001/reads.fas.CL1.aln.info | clustering/clusters/dir_CL0001/contigs.info.fasta |
22 | clustering/clusters/dir_CL0001/reads.fas.CL1.ace | clustering/clusters/dir_CL0001/contigs.ace |
23 | clustering/clusters/dir_CL0001/reads.fas.CL1.contigs.qual | clustering/clusters/dir_CL0001/contigs.qual |
24 | clustering/clusters/dir_CL0001/reads.fas.CL1.aln | clustering/clusters/dir_CL0001/contigs.aln |
25 | clustering/clusters/dir_CL0001/reads.fas.CL1.contigs | clustering/clusters/dir_CL0001/contigs.fasta |
26 | clustering/clusters/dir_CL0001/reads.fas.CL1.info | clustering/clusters/dir_CL0001/assembly.info |
27 | clustering/clusters/dir_CL0001/reads.fas.CL1.singlets | clustering/clusters/dir_CL0001/singlets.fasta |
28 | clustering/clusters/dir_CL0001/reads.fas.CL1.contigs.links | clustering/clusters/dir_CL0001/contigs.links |
29 | clustering/clusters/dir_CL0001/reads_oriented.fas | clustering/clusters/dir_CL0001/reads_selection_oriented.fasta |
30 | clustering/clusters/dir_CL0001/CL1_directed_graph.RData. | clustering/clusters/dir_CL0001/graph_layout_directed.RData |
31 | clustering/clusters/dir_CL0001/CL1_tmb.png | clustering/clusters/dir_CL0001/graph_layout_tmb.png |
32 | clustering/clusters/dir_CL0001/CL1.png | clustering/clusters/dir_CL0001/graph_layout.png |
33 | clustering/clusters/dir_CL0001/CL1.GL | clustering/clusters/dir_CL0001/graph_layout.GL |
34 | clustering/clusters/dir_CL0001/blast.csv | clustering/clusters/dir_CL0001/hitsort_part.csv |
35
36 ## v0.3.4
37 Oct 31 2019
38
39 - Classification of superclusters improved, classification now uses information about LTR/PBS for classification of Class_I elements
40
41
42 ## v0.3.2
43 Oct 9 2019
44
45 - Graphical reporting of comparative analysis added
46
47 ## v0.3.1
48 Jan 9 2019
49
50 - Improved detection of low complexity repeats and satellites with shorter monomer
51
52 ## v0.3.0
53 Oct 25 2018
54
55 - For back-compatibility, it is possible to select protein database version
56 - Databases of protein domains went public
57
58 ## v0.2.10
59 Oct 24 2018
60
61 - Protein database for Viridiplantae updated
62
63 ## v0.2.9
64 Jan 3 2018
65
66 - read depth for contigs is calculated
67 - contigs are also sorted based on genome representation
68
69 ## v0.2.8
70 Dec 18 2017
71
72 - by default assembly is done on clusters with size at least 5 reads
73 - preset option of Illumina, Illumina short and Oxford Nanopore
74 - option for analyzing Metazoa/ Viridiplantae added
75 - protein databases can be obtained **using fetch_databases.sh** script (password required)
76
77 ## v0.2.7
78 Dec 05 2017
79
80 - improved DNA database - protein domain were masked not to interfere with protein domain database
81 - another bug fix in parallelization and assembly
82 - alternative to blastx added - DIAMOND program can be used instead
83
84 ## v0.2.6
85 Nov 14 2017
86
87 - Improved classification of superclusters
88 - tables in HTML reports improved
89 - assembly is performed on low confidence satellite sequences
90 - assembly optimized, bug fix in parallelization
91
92 ## v0.2.5
93 Sep 1 2017
94
95 + More options added to _galaxy interface_ of TAREAN and RepeatExplorer2:
96 - automatic satellite filtering
97 - cluster size threshold setting
98 - keep original sequence names option
99 + Pipeline tests added
100
101 ## v0.2.4
102 Aug 10 2017
103
104 - Filtering of abundant satellite sequences
105 - Improved (more sensitive) search of protein domains
106 - bug fix in parallelization
107 - SHORT_ILLUMINA option added, this enable to analyze shorter reads (50nt) - command line only
108 - OXFORD_NANOPORE option added (experimental feature, command line only)
109
110 ## v0.2.3
111 Jun 9 2017
112
113 - some changes in standalone TAREAN
114
115 ## v0.2.2
116
117 - improved visualization of comparative analysis
118
119 ## v0.2.1
120
121 - log file is automatically copied to output and is part of archive(in galaxy)
122
123 ## v0.2.0
124
125 + Improved HTML output
126 + Updated documentation
127 + Full clustering analysis - RepeatExplorer2
128 + New features:
129 - Cap3 assembly added
130 - Comparative analysis
131 - LTR detection from contigs
132 - Custom database option
133 - Bugfix in excessive CPU usage
134 - Detection of TE protein domains
135
136 ## v0.1.1
137
138 + New features:
139 - Cluster merging
140 - Scan of clusters against DNA database (detection of rDNA, plastid, mitochondrial and contaminants)
141
142 ## v0.1.0
143
144
145