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ksahlin
/
strobealign
Aligns short reads using dynamic seed size with strobemers
MIT License
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Add -C option for appending FASTQ comment to SAM
#380
marcelm
closed
6 months ago
3
Use optimized indexing parameters
#379
marcelm
closed
6 months ago
1
Add option to add FASTQ comment to SAM output.
#378
ghuls
closed
6 months ago
0
Try extension alignment if seed appears to be ungapped
#377
marcelm
opened
6 months ago
1
Optimize parameters – second attempt
#376
marcelm
closed
6 months ago
7
Failed experiment: Use poolstl to sort randstrobes in parallel
#375
marcelm
closed
6 months ago
4
Fix first index of randstrobe start index to be always the 0th randstrobe
#374
hasin-abrar
closed
6 months ago
2
Source compiled program runs much slower than the bioconda version
#373
yanlifeng
closed
6 months ago
3
Use a 2-bit encoded reference
#372
marcelm
opened
7 months ago
0
Add --no-PG option for not outputting the PG SAM header
#371
marcelm
closed
7 months ago
1
With --details, add a SAM tag that shows the no. of identically scored best alignments
#370
marcelm
closed
7 months ago
3
Do not use --eqx in baseline comparison script
#369
marcelm
closed
7 months ago
0
Refactor aln.cpp
#368
marcelm
closed
7 months ago
3
Random paired-end alignment selection
#367
marcelm
closed
7 months ago
10
Structure of aln.cpp
#366
marcelm
opened
7 months ago
1
Test secondary alignments
#365
marcelm
closed
7 months ago
1
Choose random mapping locations for multimappers
#364
marcelm
closed
7 months ago
14
Fix matches ending too early in PAF output
#363
marcelm
closed
7 months ago
1
Let baseline comparison fail if no reads were in the input
#362
marcelm
closed
7 months ago
3
Baseline comparison CI job passes unexpectedly
#361
marcelm
closed
7 months ago
0
Assign single-end multimappers randomly to one of the candidate mapping locations
#360
marcelm
closed
7 months ago
3
Assign multimappers randomly to one of the candidate mapping positions
#359
marcelm
closed
7 months ago
0
Revert parameter tuning commits
#358
marcelm
closed
7 months ago
3
Imperfect read alignment, changing parameters does not help
#357
tprodanov
opened
8 months ago
9
Parameter for number of reads to estimate read length.
#356
ksahlin
opened
8 months ago
0
Parameter for hardmasked (removed) seeds
#355
ksahlin
opened
8 months ago
0
Optimized parameters lead to reduced mapping rate
#354
marcelm
opened
9 months ago
1
Add dumpstrobes --seeds option for writing out the full seed vector
#353
marcelm
closed
9 months ago
1
Removing parameter q and bitcount?
#352
ksahlin
opened
9 months ago
1
Slightly improve accuracy for read length 250
#351
marcelm
closed
9 months ago
1
Fix: Avoid nam id collisions that reduce accuracy
#350
marcelm
closed
9 months ago
7
Release 0.12.0
#349
marcelm
closed
7 months ago
6
Do not require strobealign to be in PATH when running tests
#348
marcelm
closed
9 months ago
1
Reduce memory usage when indexing
#347
marcelm
closed
9 months ago
1
Replace XXH64 with a simplified version
#346
marcelm
closed
9 months ago
1
Optimize parameters
#345
marcelm
closed
9 months ago
24
Fix read length estimation crash on chromosome-sized "reads"
#344
marcelm
closed
9 months ago
1
Mapping CHM13 against itself results in a crash
#343
marcelm
closed
9 months ago
0
Factor out a randstrobe_hash function
#342
marcelm
closed
9 months ago
1
Adding smaller biological datasets for mini-benchmarks
#341
ksahlin
opened
9 months ago
0
Avoid counting the seeds
#340
marcelm
opened
9 months ago
1
A new profile for read length 75
#339
marcelm
closed
9 months ago
11
Allow w_min to be zero
#338
marcelm
closed
9 months ago
1
More refactorings
#337
marcelm
closed
9 months ago
1
Speed up NAM merging a bit
#336
marcelm
closed
9 months ago
6
Two failed attempts of speeding up hit finding
#335
marcelm
closed
10 months ago
2
Duplicate alignments lead to spurious multimappers
#334
marcelm
opened
10 months ago
2
End coordinate of match in PAF output
#333
marcelm
closed
7 months ago
2
Penalize far apart pairs not more than as if they were two single ends
#332
marcelm
closed
10 months ago
3
Refactor align_PE
#331
marcelm
closed
10 months ago
1
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