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ksahlin
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strobealign
Aligns short reads using dynamic seed size with strobemers
MIT License
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Mapping accuracy: --aemb vs -x vs base-level alignment
#430
jakobnissen
opened
4 days ago
1
Closed syncmers with lower density
#429
Daniel-Liu-c0deb0t
opened
2 weeks ago
1
Make Python bindings work with nanobind 2+
#428
marcelm
closed
3 weeks ago
1
Add a debugging compilation option for showing list of NAMs
#427
marcelm
closed
3 weeks ago
1
Multi-context seeds plus fixes and optimized parameters
#426
marcelm
opened
1 month ago
3
Fix: Do not report failed alignments
#425
marcelm
closed
1 month ago
2
Entries of the unaligned
#424
u-xixi
closed
1 month ago
2
Optimized parameters for multi-context seeds
#423
marcelm
opened
1 month ago
6
Test multi-block gzip files as input
#422
marcelm
closed
1 month ago
0
strobealign: Too many reference sequences.
#421
lfdelzam
opened
1 month ago
3
Explore using Block Aligner for extension and global DP alignment
#420
Daniel-Liu-c0deb0t
opened
2 months ago
2
Do more hamming distance attempts?
#419
ksahlin
opened
2 months ago
0
Decompress with ISA-L
#418
marcelm
opened
2 months ago
3
Support for both open and closed syncmers
#417
ksahlin
opened
2 months ago
0
Lower bounding w_min to 1 instead of 0?
#416
ksahlin
opened
2 months ago
0
Joining nearby NAMs for combined score
#415
ksahlin
opened
2 months ago
1
Skip to compute merge_hits_into_nams_forward_and_reverse if nonrepetitive_fraction above threshold
#414
ksahlin
opened
3 months ago
0
Shuffle identical alignments pseudo-randomly on query name instead?
#413
ksahlin
opened
3 months ago
0
Get rid of the last compiler warning
#412
marcelm
closed
3 months ago
0
Better fix for #409
#411
drtconway
closed
3 months ago
2
Add a fix for #409
#410
drtconway
closed
3 months ago
0
Invalid @SQ header
#409
drtconway
closed
3 months ago
2
end-to-end alignment with strobalign?
#408
fplazaonate
closed
3 months ago
1
Optimize parameters (again)
#407
marcelm
opened
3 months ago
4
Huge pages on Linux
#406
marcelm
closed
3 months ago
0
Experiment: Asymmetric randstrobe hashes
#405
marcelm
opened
3 months ago
6
Make --aemb work with -o
#404
marcelm
closed
3 months ago
1
Set default number of threads to 1
#403
marcelm
closed
3 months ago
3
Version 0.13.0
#402
marcelm
closed
3 months ago
0
Change default number of threads
#401
marcelm
closed
3 months ago
1
Fix StrobemerIndex.find() in Python bindings
#400
marcelm
closed
3 months ago
0
Support end-to-end alignments?
#399
y9c
opened
4 months ago
10
Make index creation deterministic
#398
marcelm
closed
4 months ago
1
Optimize parameters
#397
marcelm
closed
3 months ago
1
Introduce canonical read length 75
#396
marcelm
closed
4 months ago
1
Optimized parameters for read length 50 decrease accuracy for read length 75
#395
marcelm
closed
4 months ago
3
strobealign-aemb module for metagenomic binning
#394
psj1997
closed
3 months ago
2
Explicit error if too many sequences are used
#393
luispedro
closed
4 months ago
3
Vendor zstr instead of fetching it from Git at build time
#392
marcelm
closed
5 months ago
1
Simplify baseline comparison on CI
#391
marcelm
closed
5 months ago
1
Fix insert size computation in is_proper_nam_pair
#390
marcelm
closed
5 months ago
1
Fix drop in mapping-only accuracy
#389
marcelm
closed
5 months ago
1
Add multi-context seeds
#388
Itolstoganov
opened
5 months ago
8
Using Strobealign for aligning RNAseq to recodonized gene
#387
Rohit-Satyam
opened
5 months ago
1
Use poolstl to sort randstrobes in parallel (attempt two)
#386
marcelm
closed
4 months ago
14
Try poolSTL again to parallelize randstrobe sorting
#385
marcelm
closed
4 months ago
1
Fix misspelled "strobealign"
#384
marcelm
closed
6 months ago
0
strobealign misspelt
#383
ksahlin
closed
6 months ago
1
Use ksw2 to align soft-clipped ends from ungapped alignment
#382
marcelm
opened
6 months ago
7
Set MAPQ=0 for secondary alignments
#381
marcelm
closed
6 months ago
1
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