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53 Open 126 Closed
53 Open 126 Closed
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Issues list

Investigating the scoring function in paired end mode
#469 opened Dec 11, 2024 by ksahlin
Question about SyncmerIterator
#463 opened Dec 2, 2024 by drtconway
4
Question: Identity threshold
#462 opened Nov 26, 2024 by stas-malavin
12
estimating breadth of coverage with strobealign --aemb
#456 opened Nov 12, 2024 by wwood
3
Reconsider the has_shared_substring heuristic
#437 opened Sep 3, 2024 by marcelm
Start indexing while still reading the reference
#436 opened Aug 22, 2024 by marcelm
All secondary alignments lost
#433 opened Aug 1, 2024 by tprodanov
7
Multiple mapping
#431 opened Jul 23, 2024 by yazhinia
4
Closed syncmers with lower density
#429 opened Jun 15, 2024 by Daniel-Liu-c0deb0t
1
Optimized parameters for multi-context seeds
#423 opened Apr 30, 2024 by marcelm
6
Explore using Block Aligner for extension and global DP alignment
#420 opened Apr 28, 2024 by Daniel-Liu-c0deb0t
2
Do more hamming distance attempts?
#419 opened Apr 24, 2024 by ksahlin
Support for both open and closed syncmers feature New feature or request
#417 opened Apr 19, 2024 by ksahlin
Lower bounding w_min to 1 instead of 0?
#416 opened Apr 18, 2024 by ksahlin
Joining nearby NAMs for combined score
#415 opened Mar 31, 2024 by ksahlin
1
Skip to compute merge_hits_into_nams_forward_and_reverse if nonrepetitive_fraction above threshold
#414 opened Mar 30, 2024 by ksahlin
Shuffle identical alignments pseudo-randomly on query name instead?
#413 opened Mar 30, 2024 by ksahlin
Optimize parameters (again)
#407 opened Mar 12, 2024 by marcelm
4
Support end-to-end alignments?
#399 opened Feb 28, 2024 by y9c
10
Try extension alignment if seed appears to be ungapped
#377 opened Dec 11, 2023 by marcelm
1
Use a 2-bit encoded reference
#372 opened Nov 30, 2023 by marcelm
Structure of aln.cpp
#366 opened Nov 20, 2023 by marcelm
1
Imperfect read alignment, changing parameters does not help
#357 opened Oct 31, 2023 by tprodanov
1
9
Parameter for number of reads to estimate read length.
#356 opened Oct 30, 2023 by ksahlin
Parameter for hardmasked (removed) seeds
#355 opened Oct 9, 2023 by ksahlin
ProTip! no:milestone will show everything without a milestone.