forked from bcgsc/abyss
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathChangeLog
1251 lines (974 loc) · 40 KB
/
ChangeLog
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
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
2015-05-28 Ben Vandervalk <[email protected]>
* Release version 1.9.0
* New paired de Bruijn graph mode for assembly.
* First official release of Sealer, a tool for closing
scaffold gaps by navigating a Bloom filter de Bruijn graph.
* New outward extension feature for Konnector to generate
long pseudo-reads.
* Support for the DIDA (Distributed Indexing Dispatched
Alignment) framework, for computing sequence alignments
in parallel across multiple machines.
* Unit tests can now be run easily with 'make check', without
external dependencies.
abyss-bloom:
* abyss-bloom 'build' command now supports -j option for
multi-threaded Bloom filter construction.
abyss-map:
* New --protein option for mapping protein sequences.
abyss-pe:
* New paired de Bruijn graph mode for assembly. Enable by
setting `k` to the k-mer pair span and `K` to size of an
individual k-mer in a k-mer pair. See README.md for further
details.
* New `aligner=dida` option for using the DIDA parallel alignment
framework. See the DIDA section of the abyss-pe man page
for usage details.
* New `graph=gfa` option to use the GFA (Graphical
Fragment Assembly) format for intermediate graph files.
abyss-sealer:
* New tool for closing scaffold gaps by navigating a Bloom
filter de Bruijn graph
* See Sealer/README.md or abyss-sealer man page for details
and examples.
konnector:
* New --extend option for extending merged and unmerged
reads outwards in the de Bruijn graph.
2014-07-09 Anthony Raymond <[email protected]>
* Release version 1.5.2
* First official release of Konnector and abyss-bloom.
* More GCC 4.8+ fixes! Modified Boost install instructions.
* Fixed rare bug when parsing output of BWA.
ABYSS:
* New option, --mask-cov, use kmers with lowercased bases, but
don't count them towards multiplicity.
abyss-bloom:
* Construct reusable Bloom filter files for use with Konnector.
* Perform boolean operations on two or more bloom filters.
Currently supports union and intersection operations.
abyss-fixmate:
* Check for boost 1.43+ when using `unordered_map::quick_erase`.
* New option, --all, to report all alignments.
* Set mate unmapped flag for mateless reads.
abyss-longseqdist:
* Fixed `error: invalid CIGAR` when reading BWA output.
configure:
* Include mpi and boost libraries as system libraries. Silences
warnings (treated as errors) when compiling with GCC 4.8+.
konnector:
* Merge read pairs into a single sequence (pseudoread) by
building a Bloom filter de Bruijn graph and searching for paths
between the paired end reads. Input reads may be
FASTA/FASTQ/SAM/BAM. The input files must be sorted by read name
and may not contain orphan reads.
2014-05-07 Anthony Raymond <[email protected]>
* Release version 1.5.1
* Fix an issue with strand-specific RNA-Seq assembly when running
`abyss-filtergraph --assemble --SS`.
* Portability fixes for Fujitsu C Compiler (FCC).
abyss-filtergraph:
* Assemble contigs in forward orientation with `--assemble --SS`
abyss-pe:
* Fix some cases where abyss-pe uses incorrect executables
ABYSS-P:
* Portability fix with FCC
2014-05-01 Anthony Raymond <[email protected]>
* Release version 1.5.0
* Assemble strand-specific RNA-Seq libraries into strand-specific
contigs.
* New parameters, Q and xtip. Improves assembly in high-coverage
regions by removing recurrent read errors.
* Portability fixes for Fujitsu C Compiler.
abyss-pe:
* New parameter, `Q`, to mask low quality bases to N.
* New parameter, `xtip=1`, to remove 2-in 0-out tips.
* New parameter, `ss=1`, to perform strand-specific assembly
using ssRNA-Seq libraries.
* New command, `scaftigs`. Breaks scaffold sequences at 'N's and
produce a scaftigs.fa file.
* Include long-scaffs.fa in FAC statistics if `long` parameter
used.
abyss-fixmate:
* Performance improvement for GCC-4.6 and older.
DistanceEst:
* Report an estimation of duplicate fragments from read pairs
mapping to different contigs.
abyss-fixmate:
* Report number of fragments removed as noise and outliers.
ABYSS/ABYSS-P:
* New option, --SS, to support strand-specific assembly.
abyss-layout:
* New option, --SS, to support strand-specific assembly.
abyss-map:
* New option, --SS, to support strand-specific assembly.
abyss-overlap:
* New option, --SS, to support strand-specific assembly.
abyss-PathOverlap:
* New option, --SS, to support strand-specific assembly.
abyss-scaffold:
* New option, --SS, to support strand-specific assembly.
* Don't prune xtips when scaffolding.
AdjList:
* New option, --SS, to support strand-specific assembly.
Overlap:
* New option, --SS, to support strand-specific assembly.
PopBubbles:
* New option, --SS, to support strand-specific assembly.
2013-11-20 Anthony Raymond <[email protected]>
* Release version 1.3.7
* Use long sequences to rescaffold scaffolds. May be run by
adding libraries to the `long’ parameter. When Scaffolding
with RNA-Seq contigs from a Trans-ABySS assembly, the genic
contiguity is greatly improved.
* Added support gcc 4.8+, and Mac OS X 10.9 Mavericks with clang.
* Licensed as GPL for non-commercial purposes.
abyss-fac:
* Added e-size to contiguity statistics as described in the GAGE
paper.
abyss-filtergraph:
* Bug fix. `--assemble’ will not fail an assertion.
* New option, --max-length, used to remove contigs over the
specified threshold.
* Trim 2-in 0-out tips when removing tips.
abyss-map:
* Bug fix. Correctly set mapq=0 for reads that multi map.
abyss-longseqdist:
* New program. Generate distance estimates between all contigs a
single read maps to.
abyss-mergepairs:
* Report number of reads chastity filtered.
abyss-overlap:
* Bug fix. Handle ambiguity codes.
abyss-pe:
* Support BWA-MEM with assembly. Run using parameter
`aligner=bwamem’.
* Added another scaffolding stage using long sequences. May be
run by adding libraries to the `long’ parameter.
ABYSS-P:
* Bug fix. Do not use awk to merge fasta files.
abyss-samtobreak:
* Building bug fix. Check that ghc modules are installed.
UnitTest:
* The Google C++ testing framework has been added to ABySS.
2013-07-15 Anthony Raymond <[email protected]>
* Release version 1.3.6
* Improved documentation for GitHub devs.
* ABYSS-P performance improvement.
* Various portability and bug fixes.
abyss-mergepairs:
* Fix program name.
abyss-fac:
* New option --exp-size to give the expected genome size needed
for NG50 calculation.
* New option --count-ambig include ambiguities in calculations.
ABYSS/ABYSS-P:
* Performance improvement. Runtime reduced by ~20%.
* Fix support for MPICH.
abyss-map:
* No longer require POPCNT instruction.
* New option --order to force output order the same as input.
abyss-filtergraph:
* New option --remove to remove specified contigs from graph.
PopBubbles:
* Bug fix. Setting branches > 2 will now work.
abyss-fixmate:
* Improved error when first and second read IDs do not match.
* New option --cov to compute and store the physical coverage in
a Wiggle file.
AdjIO:
* Bug fix for non-GCC compilers.
2013-03-04 Anthony Raymond <[email protected]>
* Release version 1.3.5
* Standardized --help message format.
* Improve documentation.
* Merge overlapping read pairs.
* Layout and merge contigs using sequence overlap graph.
* Attempt to fill scaffold gap with consensus of all paths between
contigs.
abyss-pe:
* Attempt to fill scaffold gap with consensus of all paths between
contigs.
AdjList:
* Increase the default value of m from 30 to 50.
abyss-overlap:
* Increase the default value of m from 30 to 50.
* New options, --tred and --no-tred. Remove transitive edges.
Default --tred.
abyss-mergepairs:
* New program. Merges overlapping read pairs.
ABYSS-P:
* Bug fix. Exit when there is a problem reading a file.
* Don't store sequences in the rank 0 process when using at least
1000 cores. Improves memory distribution with large number of
cores.
abyss-fac:
* Increase the default value of t from 200 to 500.
DistanceEst:
* Bug fix. Exit with success if there is only one contig. Fixes
this error:
DistanceEst: DistanceEst.cpp:534: int main(int, char**): Assertion `in' failed.
* Bug fix. Fix the bug causing this error:
DistanceEst: error: The observed fragment of size 128 bp is shorter than 2*l (l=71). Decrease l to 64.
* Bug fix. Correctly estimate distance using MLE when l=0.
abyss-layout:
* New program. Layout contigs using the sequence overlap graph.
abyss-map:
* Return helpful error when query ID starts with '@`
* New options, --chastity and --no-chastity. Ignore chastity
failed reads. Default --no-chastity.
abyss-samtobreak:
* New script. Calculate contig and scaffold contiguity and
correctness metrics.
abyss-fixmate:
* New option, l. Minimum alignment length. Set unmapped flag if
the CIGAR match length is too small.
* Print all alignments when the histogram output file not given.
* Print SAM header to the same file when given.
2012-05-30 Shaun Jackman <[email protected]>
* Release version 1.3.4.
* Do not extend paths, which can cause misassemblies.
* Increase the default value of m from 30 to 50.
* Various portability fixes.
abyss-pe:
* Increase the default value of m from 30 to 50 to reduce the
likelihood of misassemblies.
* Integrate with SLURM. Thanks to Timothy Carlson.
ABYSS:
* Use CityHash64 rather than Bob Jenkins' hashlittle.
SimpleGraph:
* Do not extend paths. Closes #8. Extending paths can cause
misassemblies when the de Bruijn graph is incomplete.
MergePaths:
* Bug fix. Closes #6. Fix the bug causing the error:
Assertion `!m_ambig' failed.
abyss-fatoagp:
* New script. Create a FASTA file of scaftigs and an AGP file.
2012-03-13 Shaun Jackman <[email protected]>
* Release version 1.3.3.
* New parameter, l. Specify the minimum alignment length when
aligning the reads to the contigs.
* Improve the scaffolding algorithm that identifies repeats.
* Improve the documentation.
abyss-pe:
* New parameter, l. Specify the minimum alignment length when
aligning the reads to the contigs. This option may be specified
per library. The default value is k.
* New parameter, S. Specify the minimum contig size required for
building scaffolds.
* New parameter, N. Specify the minimum number of pairs required
for building scaffolds.
* Integrate with Load Sharing Facility (LSF).
* Calculate the assembly contiguity statistics.
KAligner, abyss-map:
* Rename the minimum alignment length option -k to -l.
DistanceEst:
* Dual licensed under the GPL and BCCA-Academic licenses.
* New options, --fr and --rf. Specify the orientation of the
library. The default behaviour is to detect the orientation.
* New options, --mind and --maxd. Specify the minimum and maximum
distances for the maximum likelihood estimator.
* New option, -l, --min-align. Specify the minimum alignment
length of the aligner, which can improve distance estimates.
* Increase the default minimum mapping quality, -q, to 10, was 1.
MergePaths:
* Bug fix. Fix the bug causing the error:
Assertion `count(it2+1, path2.end(), pivot) == 0' failed.
PathConsensus:
* Bug fix. Fix the bug causing the error:
Assertion `fstSol.size() == sndSol.size()' failed.
MergeContigs:
* Calculate the assembly contiguity statistics.
abyss-scaffold:
* Improve the algorithm that identifies repeats.
* Remove simple cycles from the scaffold graph.
* Calculate the assembly contiguity statistics.
* The option -s may specify a range, such as -s200-10000,
to find the value of s that maximizes the scaffold N50.
abyss-fac:
* New option, -m, --mmd. Output MultiMarkdown format.
abyss-index:
* New option, -a, --alphabet. Specify the alphabet.
* New option, --bwt. Output the Burrows-Wheeler transform.
abyss-samtoafg:
* New script. Convert a SAM file to an AMOS AFG file.
README, README.html, abyss-pe.1:
* Improve the documentation.
2011-12-13 Shaun Jackman <[email protected]>
* Release version 1.3.2.
* Enable scaffolding by default.
* Remove small shim contigs.
* Improved distance estimates.
* Reduce sequence duplication.
* Read compressed files on Mac OS X.
abyss-pe:
* Enable scaffolding by default. If the mp parameter is not
specified, use a default value of ${pe} or ${lib}.
* Support using bowtie2 to align reads to contigs by specifying
aligner=bowtie2.
* The default aligner is abyss-map.
* Output the scaffold overlap graph, ${name}-scaffolds.dot.
* Set DYLD_FORCE_FLAT_NAMESPACE to read compressed files on OS X.
ABYSS:
* Can read k-mer count data from a Jellyfish file with extension
.jf for k-mer counts or .jfq for q-mer counts. Jellyfish must be
installed.
* Bug fix. Fix the bug causing the error
bool chomp(std::string&, char): Assertion `s.length() > 1' failed.
abyss-filtergraph:
* New program. Remove small shim contigs that add no useful
sequence to the assembly. Thanks to Tony Raymond (tgr).
PopBubbles:
* New option, -a, --branches. Specify the maximum number of
branches of a bubble that may be popped. Default is 2.
* Use DIALIGN-TX for multiple sequence alignment. Thanks to tgr.
DistanceEst:
* Improved distance estimates.
abyss-joindist:
* Remove this program. Use abyss-todot instead.
MergePaths:
* Use a non-greedy algorithm that reduces sequence duplication but
may reduce contiguity. The greedy algorithm may be used by
specifying the option --greedy.
abyss-fixmate:
* Do not output query names by default.
configure:
* New option, --enable-samseqqual. Enable SAM sequence and quality
fields.
2011-10-24 Shaun Jackman <[email protected]>
* Release version 1.3.1.
* Read sequence files in SRA format. The tool fastq-dump from the
sratoolkit must be installed.
* Read a contig overlap graph in the ASQG format of SGA.
* Fix compile errors for Mac OS X.
* Fix the bug that caused the line number of an error in a FASTQ
file to be reported incorrectly.
abyss-pe:
* Support using BWA-SW to align reads to contigs by specifying
aligner=bwasw.
* The parameter ALIGNER_OPTIONS may be used to specify a different
value for k when aligning using abyss-map.
* New target, bam, may be used to produce a final BAM file of the
reads aligned to the scaffolds.
KAligner:
* Fix the bug causing the error:
Assertion `qstep >= 0 && qstep <= m_hashSize' failed.
abyss-scaffold:
* The result is independent of the order in which the mate-pair
libraries are specified.
* Permit scaffolding contigs that have non-numeric identifiers.
* The overlap graph is optional.
abyss-todot:
* Convert adj, dist or ASQG formatted graph files to dot format.
* Merge multiple graph files into one.
2011-09-09 Shaun Jackman <[email protected]>
* Release version 1.3.0.
* Use mate-pair libraries to scaffold contigs.
* Support CASAVA-formatted FASTQ files.
* Bug fix. Do not trim quality 41 bases from the ends of reads.
* Boost C++ Libraries are required to compile ABySS.
abyss-pe:
* New parameter, mp, to specify the mate-pair libraries to be used
for scaffolding.
* Increase the default value for s from 100 to 200.
* Set the default value for n to 10.
* Integrate with PBS.
abyss-scaffold:
* New program. Scaffold using mate-pair libraries.
DistanceEst:
* Ignore multimapped alignments with a mapping quality of zero.
* New option, -q, --min-mapq. Ignore alignments with mapping
quality less than this threshold. Default is 1.
* Do not use OpenMP 3.0.
PopBubbles:
* Scaffold over complex bubbles with the option --scaffold.
Disabled by default.
MergePaths:
* Fix a bug that causes PathOverlap to die with the error:
Distance get(edge_bundle_t, const Graph&, ContigNode, ContigNode):
Assertion `e.second' failed.
* New option, --no-greedy. Use a non-greedy algorithm that reduces
sequence duplication but reduces contiguity. Disabled by default.
KAligner:
* Performance improvements. Thanks to Tony Raymond (tgr).
* The output is printed in the same order as the input when
multithreaded. (tgr)
abyss-map:
* New program. Use the BWT and FM-index to find the longest common
substring. To use it, specify the option aligner=map to abyss-pe.
abyss-index:
* New program. Build a FM-index of a FASTA file.
abyss-bowtie:
* Use abyss-tofastq --interleave to speed up abyss-fixmate.
abyss-bwa:
* Use bwa index -a bwtsw by default.
* Use abyss-tofastq --interleave to speed up abyss-fixmate.
abyss-fac:
* Report N80, N50 and N20. Do not report median and mean.
* Increase the default minimum contig size threshold, option -t,
from 100 to 200.
abyss-fixmate:
* Set the mapping quality of both alignments to the minimum
mapping quality of the pair of alignments.
abyss-tofastq:
* New option, -i, --interleave. Interleave the files.
configure:
* New option, --with-boost. Specify the path for Boost.
* New option, --disable-popcnt. Do not use the popcnt instruction.
2011-04-15 Shaun Jackman <[email protected]>
* Release version 1.2.7.
abyss-pe:
* Support using bwa or bowtie to align reads to contigs.
Specify aligner=bwa or aligner=bowtie.
* Integrate with IBM LoadLeveler.
PopBubbles:
* Use an affine gap penalty.
* The default maximum bubble length is 10 kbp.
* New option, --scaffold. Scaffold over bubbles with insufficient
sequence identity to be popped.
SimpleGraph:
* New parameter d to specify the acceptable error of a distance
estimate. The default is 6 bp.
PathConsensus:
* Use an affine gap penalty.
MergePaths:
* Fix a bug that causes PathOverlap to die with the error:
Distance get(edge_bundle_t, const Graph&, ContigNode, ContigNode):
Assertion `e.second' failed.
2011-02-07 Shaun Jackman <[email protected]>
* Release version 1.2.6.
* Find contigs that overlap by fewer than k-1 bp.
* Pop bubbles with sufficient sequence identity.
* Merge paths that overlap unambiguously.
abyss-pe:
* New parameter, m, the minimum number of overlapping bases.
The default is 30.
* The minimum sequence identity parameter, p, applies to both
PopBubbles and PathConsensus.
ABYSS:
* Support values of k larger than 96. The maximum value of k is
set when compiling using `configure --enable-maxk´.
AdjList:
* Find sequences that overlap by fewer than k-1 bp. The parameter
m specifies the minimum number of overlapping bases.
PopBubbles:
* Align both branches of the bubble and pop bubbles whose sequence
identity is sufficient, at least 90% by default.
* New parameter, p, the minimum identity required.
* The maximum bubble size is unlimited by default. This limit can
be changed using the parameter b.
SimpleGraph:
* Extend each path as long as is unambiguously possible.
PathOverlap:
* Merge paths that overlap unambiguously.
MergeContigs:
* Perform an alignment of the two sequences when no simple overlap
is found.
abyss-fac:
* New option, -g. Specify the expected genome size.
2010-11-15 Shaun Jackman <[email protected]>
* Release version 1.2.5.
AdjList:
* Fix the colour-space-specific bug causing the error
Assertion `seq.length() > (unsigned)opt::overlap' failed.
PathConsensus:
* Fix the bug causing the error
Assertion `fstSol.size() == 1' failed.
abyss-fixmate:
* Do not output the @RG header record at the end of the output
that gives the median fragment size. It breaks `samtools view -S`.
* --no-qname: New option. Set the qname to *.
2010-10-13 Shaun Jackman <[email protected]>
* Release version 1.2.4.
ABYSS-P:
* Fix the bug causing the error
Unexpected sequence extension message.
KAligner:
* Reduce the amount of memory used by KAligner.
PathConsensus:
* New program. Replace gaps of Ns that span a region of ambiguous
sequence with a consensus sequence of the possible sequences that
fill the gap. By default a minimum 90% identity is required. This
default can be changed with the parameter, p. The consensus
sequence uses IUPAC-IUB ambiguity codes. DIALIGN-TX is used for
the multiple sequence alignment.
PathOverlap:
* Fix the bug causing the error
Assertion `back(paths, u) == front(paths, v)' failed.
2010-09-08 Shaun Jackman <[email protected]>
* Release version 1.2.3.
ABYSS-P:
* Bug fix. Fix the bug causing the error
Assertion `m_comm.receiveEmpty()' failed.
PopBubbles:
* Bug fix. Fix the bug causing the error
error: unexpected ID
PathOverlap:
* Include the single-end contigs in the overlap graph.
abyss-pe:
* Output an overlap graph of the paired-end assembly in the file
${name}-contigs.dot.
* Do not create the intermediate file ${name}-4.fa.
abyss-adjtodot:
* Convert an overlap graph in adj format to Graphviz dot format or
SAM alignment format.
2010-08-25 Shaun Jackman <[email protected]>
* Release version 1.2.2.
* Merge contigs after popping bubbles.
* Handle multi-line FASTA sequences.
* Report the amount of memory used.
* Most tools can output their results in SAM format, including
AdjList, KAligner, ParseAligns and PathOverlap.
abyss-pe:
* New command, se-dot. Output a Graphviz dot file of the
single-end assembly.
ABYSS:
* Handle multi-line FASTA sequences.
* Report the amount of memory used.
* Improve error messages for incorrectly-formatted FASTA files.
* Bug fix. Improved handling of palindromes.
PopBubbles:
* Merge contigs after popping bubbles.
* Bug fix. Do not pop bubbles resulting from palindromes.
KAligner:
* Report the amount of memory used.
* New option, --sam. Output the alignments in SAM format.
ParseAligns, DistanceEst:
* Bug fix. The CIGAR string was oriented with respect to the
query rather than with respect to the target, which is standard.
AdjList, PathOverlap:
* New option, --sam. Output the adjacency graph in SAM format.
abyss-fixmate:
* New program. Similar to samtools fixmate, but does not require
that the input be sorted by query ID, although it is faster if it
is sorted.
2010-07-12 Shaun Jackman <[email protected]>
* Release version 1.2.1.
* Handle reverse-forward oriented mate pair libraries.
* Improved distance estimates, particularly with large fragment
libraries.
abyss-pe:
* New commands:
se-contigs: Assemble single-end contigs.
pe-contigs: Assemble paired-end contigs (default).
se-sam: Output a gzipped SAM file of the single-end assembly.
se-bam: Ouptut a BAM file of the single-end assembly.
pe-dot: Output a Graphviz dot file of the paired-end assembly.
all: Sam as se-bam pe-contigs pe-dot.
* Options for one particular library may be specified:
lib='lib1 lib2' lib2_s=1000 lib2_n=25
* Input sequence may come from an arbitrary command, which is
useful to assemble a region of an aligned BAM file:
in='<(samtools view genome.bam chr10)'
ABYSS:
* Bug fix. When reading SAM/BAM files, the quality format
incorrectly defaulted to ASCII-64, when it should be ASCII-33.
ABYSS-P:
* May use the Intel MPI library.
ParseAligns:
* Count the number of forward-reverse, reverse-forward and
forward-forward oriented alignments.
DistanceEst:
* Handle reverse-forward oriented mate pair libraries.
* Improved distance estimates, particularly with large fragment
libraries.
* Remove duplicate mate pairs.
* Print a pretty UTF-8 bar plot of the fragment-size distribution.
* Multithreaded using OpenMP. The -j, --threads option specifies
the number of threads to use.
* Performance improvment.
Overlap:
* Handle cases when more than one gap occurs within the mate pair
fragment size.
SimpleGraph:
* Performance improvment.
MergePaths:
* Handle the case when a circular sequence is assmembled into a
single contig.
abyss-tofastq:
* New program. Convert qseq, export, SAM and BAM files to FASTA or
FASTQ format. The files may be compressed with gz, bz2 or xz and
may be tarred.
2010-05-25 Shaun Jackman <[email protected]>
* Release version 1.2.0.
* Scaffold over gaps in coverage and unresolved repetitive
sequence using Ns.
* Read sequence from SAM and BAM files.
abyss-pe:
* Set q=3 by default. Trim bases from the ends of reads whose
quality is less than 3.
* Do not store the .pair.gz file.
* Generate a BAM file of the mate pairs that align to
different contigs of the single-end assembly. Disabled by default.
* Output a Graphviz dot file of the paired-end assembly.
Disabled by default.
* Store the bubbles in ${name}-bubbles.fa rather than bubbles.fa.
* Store the indel bubbles in ${name}-indel.fa.
* Bug fix for mawk.
ABYSS:
* Set -E0 when coverage is low (<2).
ABYSS-P:
* Remove the temporary files contigs-*.fa and snp-*.fa.
PopBubbles:
* Output in Graphviz dot format using --dot.
KAligner:
* Do not ignore sequences (reads or contigs) containing N.
* Output SAM headers (but not SAM alignments).
ParseAligns:
* Output in SAM format.
DistanceEst:
* Input in SAM format.
* Output in Graphviz dot format using --dot.
Overlap:
* Scaffold over gaps in coverage. Scaffolding can be disabled
using the option --no-scaffold.
* Merge contigs that overlap at simple repeats. These merges can
be prevented using the option --no-merge-repeat.
SimpleGraph:
* Scaffold over repeats. Scaffolding can be disabled using the
option --no-scaffold.
MergePaths:
* Merge paths containing ambiguous sequence.
* Multithreaded using OpenMP. The -j, --threads option specifies
the number of threads to use.
MergeContigs:
* Merge paths and contigs containing ambiguous sequence.
PathOverlap:
* Output in Graphviz dot format using --dot.
Consensus:
* Output the pileup in samtools format.
2010-02-15 Shaun Jackman <[email protected]>
* Release version 1.1.2.
ABYSS:
* Read tar files including compressed tar files.
* New parameter -b, --bubble-length=N. Pop bubbles shorter than
N bp. The default is b=3*k.
AdjList:
* Include the contig coverage in the output.
* The script abyss-adjtodot converts an ABySS adjacency file to
GraphViz dot format.
PopBubbles:
* Pop bubbles resulting from indels.
KAligner:
* Synchronize the threads periodically (every ten thousand
alignments by default) to ease the computational burden on
ParseAligns. This synchronization can be disabled using --sync=0.
* Use two threads by default.
abyss-pe:
* New parameter, b.
* Use two threads by default.
* The read length argument, l, is deprecated. To emulate the
behaviour of ABySS 1.0.14 and older, set t=6*(l-k+1). The default
is t=k.
2010-01-19 Shaun Jackman <[email protected]>
* Release version 1.1.1.
ABYSS:
* Pop complex bubbles either completely or not at all. Bubble
popping now completes in a single round.
* Choose better (typically lower) default values for the
parameters -e,--erode and -c,--coverage. The default threshold is
the square root of the median k-mer coverage.
2009-12-18 Shaun Jackman <[email protected]>
* Release version 1.1.0.
* The output format of AdjList, DistanceEst and SimpleGraph has
changed to be more humanly readable.
ABYSS:
* New options, -q, --trim-quality. Trim bases from the ends of
reads whose quality is less than the specified threshold.
--standard-quality: zero quality is `!' (33)
default for FASTQ files
--illumina-quality: zero quality is `@' (64)
default for qseq and export files
Thanks to Tony Raymond.
SimpleGraph:
* Multithreaded. The -j, --threads option specifies the number of
threads to use.
* Expand tandem repeats when it is possible to determine the exact
number of the repeat.
MergePaths:
* Bug fix. A repeat that is larger than the fragment size could
be misassembled. Thanks to Tony Raymond.
abyss-pe:
* Determine the parameter j (number of threads) by finding the
number of slots allocated on the head node in the PE_HOSTFILE.
* Store the k-mer coverage histogram in coverage.hist.
2009-11-13 Shaun Jackman <[email protected]>
* Release version 1.0.16.
* Improve the performance and memory usage of KAligner and
AdjList, particularly for very large data sets.
KAligner:
* Improve memory usage when maxk is 32 or 96. No change when maxk
is the default 64.
* New option, -i, --ignore-multimap. Ignore any duplicate k-mer in
the target sequence. Thanks to Tony Raymond.
AdjList:
* Improve performance for very large data sets.
ParseAligns:
* For reads whose ID begins with `SRR', expect that the forward
and reverse read have identical ID and no suffix, such as
/1 and /2.
2009-10-19 Shaun Jackman <[email protected]>
* Release version 1.0.15.
ABYSS:
* New options, -e, --erode and -E, --erode-strand.
The parameter e erodes bases at the ends of blunt contigs with
coverage less than the specified threshold.
The parameter E erodes bases at the ends of blunt contigs with
coverage less than the specified threshold on either strand.
* New feature. If the parameters e and c are not specified,
attempt to choose appropriate values based on the observed k-mer
coverage. This feature will work best for higher coverage data.
For lower coverage data, setting e=c=2 is reasonable.
* New option, --trim-masked. Removed masked (lower case) sequence
at the beginning and end of the read. Disable with
--no-trim-masked.
* The read length, l, is an optional parameter. If the read length
is specified, the trim parameter, t, will default to 6*(l-k+1), as
before. If the read length is not specified, t will be set to the
same value as k. For longer reads or when k is less than 85% of l,
it should not be necessary to specify l. The parameter t may be
specified directly if desired.
DistanceEst:
* Bug fix. The standard deviation could be calculated incorrectly
for larger numbers, particularly for libraries with large fragment
sizes. Thanks to Tony Raymond.
Overlap:
* Bug fix. If Overlap found mate pairs on the same contig with
incorrect orientation, it would generate a misassembled contig.
These misassembled contigs are easily identified in the
xxx-3-overlap.fa file. The two contigs IDs, in the fourth and
fifth column, will be identical.
* New option, --mask-repeat. If two contigs are joined by mate
pairs and are found to overlap by a simple repeat so that the
exact number of the repeat is unknown, join the contigs estimating
the number of the repeat, and mask (lower case) the repeat
sequence. This feature is disabled by default.
abyss-pe:
* Use gunzip -c rather than zcat for portability.
configure:
* New option, --enable-mpich. Use the MPICH2 MPI library.
2009-09-08 Shaun Jackman <[email protected]>
* Release version 1.0.14.
* Read files compressed with xzip (.xz) and compress (.Z).
abyss-pe:
* Assemble multiple libraries with different fragment sizes.
* New manual page.
ABYSS:
* Don't necessarily discard reads that contain an N. Keep those
k-mer that do not contain an N.
ABYSS-P:
* Serially renumber the contigs output by ABYSS-P using awk.
2009-08-26 Shaun Jackman <[email protected]>
* Release version 1.0.13.
* Read files compressed with gzip (.gz) or bzip2 (.bz2).
ABYSS-P:
* Bug fix. Fix a race condition in the erosion algorithm.
2009-08-18 Shaun Jackman <[email protected]>
* Release version 1.0.12.
abyss-pe:
* Both ABYSS and KAligner are run only once per assembly, which
speeds up the paired-end assembly by nearly a factor of two.
* The k-mer coverage information is correct in every contig file.