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OndrejSladky
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kmercamel
KmerCamel🐫 provides implementations of several algorithms for efficiently representing a set of k-mers as a masked superstring.
MIT License
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KmerCamel supports k up to 127.
#74
OndrejSladky
opened
10 hours ago
0
Include large KmerCamel
#73
OndrejSladky
closed
11 hours ago
0
Refactoring AC code to a separate directory to simplify code structure.
#72
GordonHoklinder
closed
11 hours ago
0
Draft: Improvements in parser
#71
OndrejSladky
closed
1 week ago
0
Runs bug
#70
PavelVesely
closed
6 months ago
0
Minimization of number of ones can optionally skip the ILP part.
#69
OndrejSladky
closed
6 months ago
0
KmerCamel can compute lower bounds on superstring lengths.
#68
OndrejSladky
opened
6 months ago
2
Revert "KmerCamel can compute lower bounds on superstring lengths."
#67
OndrejSladky
closed
6 months ago
0
Optimizing the number of runs approximately without running the ILP
#66
PavelVesely
closed
6 months ago
3
output of mask optimization is not FASTA
#65
PavelVesely
closed
6 months ago
5
Different hashing for k-mers
#64
OndrejSladky
closed
7 months ago
3
Fix compilation on OS X with M1
#63
karel-brinda
closed
7 months ago
0
Compilation doesn't work on OS X with M1 because of different brew paths
#62
karel-brinda
closed
7 months ago
2
KmerCamel can minimize number of runs of ones.
#61
OndrejSladky
closed
7 months ago
2
KmerCamel can optimize masks.
#60
OndrejSladky
closed
7 months ago
0
KmerCamel can compute lower bounds on superstring lengths.
#59
OndrejSladky
closed
6 months ago
3
Added flag for turning off the memory optimizations
#58
OndrejSladky
closed
7 months ago
0
Support for k-mers with 31 < k < 64
#57
OndrejSladky
closed
7 months ago
0
Project cleanup and reorganization
#56
OndrejSladky
closed
7 months ago
0
Using khash in parsing and in local
#55
OndrejSladky
closed
7 months ago
0
Put unittests into a separate folder
#54
OndrejSladky
closed
7 months ago
1
Use khash in local
#53
OndrejSladky
closed
7 months ago
0
Use khash in parser
#52
OndrejSladky
closed
7 months ago
0
Add support for larger k-mers
#51
OndrejSladky
closed
7 months ago
0
Optimized local
#50
OndrejSladky
closed
8 months ago
0
More systematic printing of version and not requiring git
#49
OndrejSladky
closed
10 months ago
0
Improved help in convert_superstring
#48
OndrejSladky
closed
8 months ago
3
convert_superstring.py
#47
karel-brinda
closed
8 months ago
0
Version
#46
OndrejSladky
closed
10 months ago
7
Versioning
#45
karel-brinda
closed
10 months ago
1
Add general support for parsing .gz files
#44
karel-brinda
closed
1 week ago
3
The program cannot read from stdin
#43
karel-brinda
closed
1 week ago
0
The example in the program info doesn't work
#42
karel-brinda
closed
10 months ago
1
Global algorithm performance improvements
#41
OndrejSladky
closed
11 months ago
0
[convert_superstring] Optional reading masked superstring from file
#40
OndrejSladky
closed
11 months ago
0
Update README.md
#39
PavelVesely
closed
1 year ago
1
Performance improvements
#38
GordonHoklinder
closed
11 months ago
0
CLI flags for algorithms renamed.
#37
GordonHoklinder
closed
1 year ago
1
AC optimization (reading fasta using kseq.h & slightly improved re-allocations)
#36
GordonHoklinder
closed
1 year ago
1
Suboptimal C++ string handling degrades the performance of Ahomaton-based algs
#35
karel-brinda
closed
10 months ago
7
Kmercamel should fail when non-sense parameters are used
#34
karel-brinda
closed
1 year ago
2
Streaming algorithm
#33
GordonHoklinder
closed
1 year ago
0
Create ci.yml
#32
GordonHoklinder
closed
1 year ago
0
Cleanup
#31
GordonHoklinder
closed
1 year ago
0
Pseudosimplitigs and GREEDY with AC support complements
#30
GordonHoklinder
closed
1 year ago
0
Removed time from output fasta header.
#29
GordonHoklinder
closed
1 year ago
0
computation is not reproducible even on the same computer
#28
karel-brinda
closed
1 year ago
1
make test: ValueError: not enough values to unpack (expected 2, got 0)
#27
karel-brinda
closed
11 hours ago
3
error: use of undeclared identifier 'get_current_dir_name'
#26
karel-brinda
closed
1 year ago
1
Greedy should now consume less memory
#25
GordonHoklinder
closed
1 year ago
0
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