forked from ndaniel/fusioncatcher
-
Notifications
You must be signed in to change notification settings - Fork 0
/
NEWS
executable file
·339 lines (298 loc) · 16.8 KB
/
NEWS
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
Version Release History for FusionCatcher
=========================================
Version 1.35 -- 30 June 2022
----------------------------
* add support for Ensembl version 106
* fixed minor bugs
Version 1.33 -- January 22, 2021
---------------------------------
* increased sensitivity for TLX1, TLX2, and TLX3 fusions
* added support for using only the first N reads in case for very large FASTQ files
* added a required dependency to FASTQTK tool: https://github.com/ndaniel/fastqtk
* fixed several major/minor bugs
* updated manual
Version 1.30 -- December 14, 2020
---------------------------------
* added support for Ensembl version 102
* added VCF format support for outputing the found candidate fusion genes
* increased sensitivity for TLX3 fusions
* fixed several major/minor bugs
* updated manual
Version 1.20 -- November 8, 2019
--------------------------------
* added support for Ensembl version 96, 97, and 98
* increased sensitivity by adding an extra anchor
* added --limitOutSJcollapsed for better control of STAR aligner
* fixed memory bug leading to seg-fault in STAR aligner
* improved handling of low entropy reads
* size of built files for different organisms has been reduced
* fixed several minor bugs
* updated manual
Version 1.10 -- April 10, 2019
--------------------------------------
* added support for Ensembl version 91, 92, 93, 94, and 95
* fixed bug regarding randomness of mapping for Bowtie and STAR aligners
* fixed bug regarding low complexity of fusion junction sequences
* label for rt-circRNAs
* fixed several minor bugs
* updated manual
Version 1.00 - December 8, 2017
---------------------------------------
* fixes for supporting Ensembl 90
* increased sensitivity for IGH fusions
* fixed bug regarding viral sequences when building new files for a new organism
* fixed several minor bugs
* updated manual
Version 0.99.7d beta - October 30, 2017
---------------------------------------
* added support for Ensembl version 90
* fixed several minor bugs
* updated manual
Version 0.99.7c beta - June 30, 2017
---------------------------------------
* added support for Ensembl versions 87, 88, and 89
* added support for optionally forcing the execution of tools/scripts by using the corresponding absolute paths from the configuration file
* added support for two versions of Bowtie aligner, that are 1.1.2 and 1.2
* increased sensivity for certain types of IGH fusions and certain sizes of input reads
* predicted full sequences of fusion transcripts are given for cases when the fusion is in-frame
* candidate fusion genes are labelled now with exon-exon when the fusion junction is using known exon borders
* fixed bug affecting very long reads (e.g. MiSeq reads)
* fixed bug affecting single-end reads
* fixed bug which affects in rare cases the prediction of fusion junction
* fixed several minor bugs
* updated manual
Version 0.99.7b beta - February 24, 2017
---------------------------------------
* fixed a rare bug affecting 'bowtie --ff --tryhard'
* fixed several minor bugs
* updated manual
Version 0.99.7a beta - February 17, 2017
---------------------------------------
* added support for Ensembl version 86
* speed improvements
* added support for more databases of known fusion genes
* fixed a rare bug affecting split-fast.py
* fixed bug affecting the PATHs for some of tools used by FusionCatcher
* fixed bug regarding ZIP64
* added fixes from https://github.com/yhoogstrate
* fixed several minor bugs
* updated manual
Version 0.99.6a beta - May 8, 2016
---------------------------------------
* added support for Ensembl version 84
* improved handling of pseudogenes
* added support for Saccharomyces Cerevisiae organism
* more tuning for the parameters for finding fusions which involve IGH loci
* added to installation test for CRLF2-IGH@ and DUX4-IGH@ fusions
* default aligners to be used can now be set also by configuration file 'fusioncatcher/etc/configuration.cfg'
* fixed a bug regarding memory allocation when multiple threads are used
* limiting the maximum memory to maximum of 26 GB used by sort command (from coreutils)
* fixed several minor bugs
* updated manual
Version 0.99.5a beta - January 15, 2016
---------------------------------------
* added support for Ensembl version 83 and human genome GRCh38.p5
* fixed a bug which affected the sensitivity of finding fusions which involve IGH loci
* default number of threads/CPUs to be used can now be set also by configuration file 'fusioncatcher/etc/configuration.cfg'
* added to the installation test the IGH@-MALT1 fusion
* added support for STAR v2.5.0c aligner
* fixed several minor bugs
* updated manual
Version 0.99.4e beta - December 8, 2015
-----------------------------------------
* added support for Ensembl version 82
* increased sensitivity for fusion genes which involve IGH loci
* added support for database of candidate gene fusions found in healthy human RNA-seq samples from 27 different tissues http://www.mcponline.org/content/13/2/397
* added support for GTEx database (with help of FusionAnnotator)
* fixed a bug which was introducing a large runtime-slowdown when candidate IGH translocations are found
* fixed several minor bugs
* updated manual
Version 0.99.4d beta - September 15, 2015
-----------------------------------------
* added support for Ensembl version 81 and human genome GRCh38.p3/hg38.p3
* fixed bug where input reads longer than 130 bp would produce very large number of
found fusions
* increased sensitivity for fusion genes which involve IGH loci
* fixed a bug affecting the building of index/build files for non-human organisms
* fixed several minor bugs
* updated manual
Version 0.99.4c beta - June 24, 2015
-------------------------------------
* added support for Ensembl version 80
* added support for fusion genes from paper: D. Robinson, Integrative Clinical
Genomics of Advanced Prostate Cancer, Cell, Vol. 161, May 2015, doi:10.1016/j.cell.2015.05.001
* increased sensitivity for fusion genes involving IGH/IGK/TRA/TRB/TRG loci
* new output file which reports viruses/bacteria/phages found in the input data
* added support for fusion genes known to appear in non-tumor cell lines (e.g. HEK293 cells)
* added support for long (>150 bp) for single-end reads
* improved support for long (>150 bp) paired-end reads from Illumina sequencers
* fixed bug which may have caused script parallel_blat.py to run for days or even hang in cases
when very large number (>5000) of candidate fusion genes are found
* fixed several minor bugs
* updated manual
Version 0.99.4b beta - May 14, 2015
-------------------------------------
* added support for Gencode annotation release 22
* fixed bug affecting fusion genes which involve IG loci
* added installation test script (for human genome only)
* fixed several minor bugs
* updated manual
Version 0.99.4a beta - March 18, 2015
-------------------------------------
* added support for fusion genes from paper: C. Klijn, A comprehensive
transcriptional portrait of human cancer cell lines, Nature Biotechnology,
Dec. 2014, doi:10.1038/nbt.3080
* added support for Ensembl version 79 and human genome GRCh38.p2/hg38.p2
* added a very short summary of candidate fusions found in 'short_summary.txt'
* increased sensitivity for method using BOWTIE2 aligner
* fixed bug affecting PATH variable for sratoolkit
* fixed bug affecting input/output paths which contain comma(s)
* fixed bug affecting the frame prediction for found candidate fusion genes
* fixed several minor bugs
* updated manual
Version 0.99.3e beta - November 14, 2014
----------------------------------------
* fixed bug regarding memory allocation for BOWTIE2 aligner
* fixed bug regarding detection of Python version
* fixed bug regarding conversion to GRCh37/hg19 coordinates
* fixed bug where too many preliminary candidate fusions (due to usage of lower
thresholds than the default ones) would lead to no fusions been found
* fixed several minor bugs
* updated manual
Version 0.99.3d beta - November 4, 2014
---------------------------------------
* added support for BOWTIE2 aligner http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
* sensitivity and precision improved slightly (due to addition of fourth read aligner, that is BOWTIE2, in addition to BOWTIE, BLAT, and STAR)
* added automatic conversion of fusion genes coordinates to GRCh37/hg19 (only for human genome)
* added support for producing SAM files for found fusion genes which may be used for visualization purposes
* added support for FASTQ files containing reads of different sizes
* improved validation of input FASTQ files
* fixed bug where different environment settings affected the sorting of reads
* fixed bug regarding several public annotation databases, where several very well known somatic fusion transcripts (e.g. GOPC-ROS1, FIP1L1-PDGFRA, etc.) are annotated as belonging to only one gene (instead of two genes as expected)
* fixed bug regarding PSL visualization using BLAT aligner
* fixed bug where read-only input files would produce a crash
* fixed bug regarding conflits in PYTHONPATH due to OpenPYXL
* fixed several minor bugs
* updated manual
Version 0.99.3c beta - October 9, 2014
--------------------------------------
* added support for STAR aligner http://code.google.com/p/rna-star/ (STAR is used only and only for splitting reads while mapping)
* added support for latest version of Ensembl database http://www.ensembl.org (that is version 77)
* added support for latest version GRCh38/hg38 of human genome from Ensembl, RefSeq, and UCSC databases
* added suport for database of gene fusions found in TCGA database http://cancergenome.nih.gov/
* added suport for database of candidate gene fusions found in healthy human RNA-seq samples from Illumina BodyMap2 http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-513/
* added support for Duplicated Genes Database (DGD) http://dgd.genouest.org/
* added support for SeqTK tools http://github.com/ndaniel/seqtk/
* added support for COSMIC database version 70 http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/
* sensitivity and precision improved slightly (due to addition of third read aligner, that is STAR, in addition to BOWTIE and BLAT)
* added prediction of fusion protein sequences of candidate fusion genes
* slight speed improvements (due to usage of SeqTK tools)
* slightly reduced disk space requirements for temporary files
* fixed bug regarding blat_parallel.py script (in case of very few unmapped input reads and very large number of threads/CPUs)
* fixed bug regarding effect prediction of candidate fusion genes
* fixed several minor bugs
Version 0.99.3b beta - June 27, 2014
------------------------------------
* added effect prediction of fusion gene (e.g. in-frame, out-of-frame, etc.)
* fixed a bug due to Bowtie and BLAT limitation of building indexes for reference sequences with size over 2^32
* fixed bug regarding the hard links created on different devices
* fixed several minor bugs
Version 0.99.3a beta - April 15, 2014
-------------------------------------
* added support for latest version of Ensembl database http://www.ensembl.org (that is version 75)
* added support IMGT/HLA Database http://www.ebi.ac.uk/ipd/imgt/hla/ for filtering purposes (optional)
* added as known false-positive fusion genes, the fusion genes found in Illumina Body Map RNA-seq dataset
* fixed several minor bugs
Version 0.99.2 beta - February 5, 2014
--------------------------------------
* added full virus/bacteria/phages names when reporting the reads mapping on them for filtering purposes
* added option to save as FASTQ file, for later use, the unmapped reads (i.e. reads which do not map on genome, transcriptome, viruses, phages, and bacteria)
* added option to save as SAM file, for later use, the reads mapping on genomes of viruses/bacteria/phages (from the NCBI database)
* added support for UCSC database
* added support for RefSeq NCBI database
* added support for C19MC miRNA cluster
* added batch mode (i.e. fusioncatcher-batch.py)
* slightly reduced the disk space requirements for the temporary files
* improved error reporting when analyzing broken FASTQ files
* fixed several minor bugs
Version 0.99.1 beta - December 4, 2013
--------------------------------------
* added support for the latest version of Ensembl database http://www.ensembl.org (that is version 74)
* all viruses/bacteria/phages found to have reads mapping on their genomes will be listed together with the corresponding reads counts
* speed improvements when using BLAT aligner
* added support for filtering out the reads which map on Phage phiX174 genome (it is used by several sample preparation protocols for Illumina NGS)
* fixed several minor bugs
Version 0.99 beta - September 5, 2013
-------------------------------------
* added support for the latest version of Ensembl database http://www.ensembl.org (that is version 73)
* added support for the latest version of CGP database
* filtering out the reads which map on genomes of viruses/bacteria/phages (from NCBI database)
* added support for NCBI database
* added support for sorting in parallel
* fixed several minor bugs
Version 0.98 beta - June 26, 2013
---------------------------------
* added support for the latest version of Ensembl database http://www.ensembl.org (that is version 72)
* added support for Velvet v1.2.10
* reads containing short tandem repeats are filtered out
* improved support for mouse and rat organisms
* poly ends of reads are trimmed
* fixed several minor bugs
Version 0.97 beta - April 9, 2013
---------------------------------
* reads are trimmed automatically to 60 bp instead of 50 bp long as previously was done when
using the BOWTIE aligner
* added suport for the latest version of TICdb database <http://www.unav.es/genetica/TICdb/>
* added support for Cancer Genome Project (CGP) translocations database
<http://www.sanger.ac.uk/genetics/CGP/Census/>
* more labels added for labeling the fusion genes
* increased sensitivity for finding fusions genes (e.g. filtering out partially overlapping genes on the same strand)
* fixed several minor bugs
Version 0.96 beta - March 7, 2013
---------------------------------
* fusion genes which are readthroughs are considered for analysis by default
now (it can still be skipped if necessary); previously it was necessary to
specify it clearly in order for FusionCatcher to search also for
readthroughs too!
* sensitivity of finding fusion genes has been increased by decreasing the default anchor length
* BLAT aligner is used be default now (it can be disabled if necessary)
* speed improvements when using BLAT aligner
* added support for COSMIC database <http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/>
* added support for TICdb database <http://www.unav.es/genetica/TIC2/>
* added support for ChimerDB 2.0 database <http://ercsb.ewha.ac.kr/FusionGene/index.jsp> (literature-based annotation)
* added support for ConjoinG database <http://metasystems.riken.jp/conjoing/>
* known fusion genes are labeled in the final list of candidate fusion genes
* fixed several minor bugs
Version 0.95 beta - January 25, 2013
------------------------------------
* *NOTE*: it needs a newer `build data` gotten with 'fusioncatcher-build' version 95
* improved the detection rate for finding fusion genes (genes and their
corresponding pseudogenes are filtered out from the preliminary list of
candidate fusions genes)
* fixed bug regarding the *`FusionCatcher`* crashing when no fusion genes
were found
* Ensembl version 70 supported
* fixed several other minor bugs
Version 0.94 beta - December 21, 2012
-------------------------------------
* NOTE: it needs a newer built data gotten with 'fusioncatcher-build'
version 94 (in case that one already has an older built data obtained with
version 93 then one easily may upgrade it by running upgrade93to94.py in
the old built data path)
* added support for SRA toolkit version 2.2.2a
* added support for Bowtie 0.12.9
* added support for de novo assembling the support reads using Velvet
* improved the detection rate for finding fusion genes
* candidate fusion genes are filtered out early if they contain a gene and its corresponding pseudogene
* fixed bug regarding the automatic removal of adapters in case that no adapters were found
* improved the support for BLAT aligner when BLAT is used for finding candidate fusion genes
* supporting reads are also provided now in case that BLAT is used for finding fusion genes
* Ensembl version 69 supported
* fixed several other bugs
Version 0.93 beta - December 18, 2011
-------------------------------------
* First public release of FusionCatcher.
* Includes the two core tools: the builder 'fusioncatcher-build',
the fusion genes finder 'fusioncatcher'
* FASTQ/SRA inputs supported
* added support for Ensembl database version 69