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eaasna
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valik
Local sequence similarity search tool
BSD 3-Clause "New" or "Revised" License
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Generic alignment file I/O
#124
eaasna
closed
6 days ago
1
[Fix] Inclusive comparison of k-mer occurrence counts
#123
eaasna
closed
2 weeks ago
1
Dismiss low entropy patterns
#122
eaasna
closed
2 weeks ago
0
Repeat filtering: search in bins with highest entropy
#121
eaasna
opened
2 weeks ago
1
Count segment minimisers in parallel
#120
eaasna
closed
1 week ago
1
Fixup consolidate
#119
eaasna
closed
3 weeks ago
1
Distributed search
#118
eaasna
opened
3 weeks ago
0
Cleanup output
#117
eaasna
closed
3 weeks ago
1
Try to count segment minimisers in parallel
#116
eaasna
closed
3 weeks ago
1
Update E-value calculations based on BLAST 2.16
#115
eaasna
closed
1 month ago
1
Remove raptor data simulaiton submodule
#114
eaasna
closed
1 month ago
1
Print warning for verbose output
#113
eaasna
closed
1 month ago
1
Trim ID after first whitespace
#112
eaasna
closed
1 month ago
1
Debug bucket borders
#111
eaasna
opened
1 month ago
0
Suggestions from code review
#110
eaasna
closed
1 month ago
1
Remove duplicate alphabets and replace seqan2::String
#109
eaasna
opened
4 months ago
1
Runtime log
#108
eaasna
closed
1 month ago
0
Fix detailed runtime log
#107
eaasna
closed
4 months ago
1
Precompute minimisers for k-mer count filtering
#106
eaasna
closed
5 months ago
1
Always preprocess reference sequences for reference size dependant parameter deduction
#105
eaasna
closed
6 months ago
1
Find FNR for heuristic threshold
#104
eaasna
closed
8 months ago
1
Debug kmers
#103
eaasna
closed
8 months ago
0
Do not write empty Stellar files
#102
eaasna
opened
11 months ago
0
Refactor the argument parser
#101
eaasna
closed
11 months ago
1
[FIX] Remove whitespace from FASTA id
#100
eaasna
closed
1 year ago
0
[INFRA] Update license
#99
eaasna
closed
1 year ago
1
Do not allow shared memory metagenome search
#98
eaasna
closed
1 year ago
1
Search vs consolidation time
#97
eaasna
closed
1 year ago
1
Join metadata tables into a single file
#96
eaasna
closed
1 year ago
1
Incorporate match consolidation into search
#95
eaasna
closed
1 year ago
1
Error rate instead of number of errors
#94
eaasna
closed
1 year ago
0
Split query database
#93
eaasna
closed
1 year ago
1
Shared memory mode: pass queries in memory
#92
eaasna
closed
1 year ago
1
[FIX] Stellar DNA4 alphabet
#91
eaasna
closed
1 year ago
1
Call Stellar search functions
#90
eaasna
closed
1 year ago
1
fix: processing local data, locally inside of valik_search
#89
SGSSGene
closed
1 year ago
0
[FIX] clean up stellar3 arguments and valik argument parsing
#88
eaasna
closed
1 year ago
1
[FIX] clean up stellar3 arguments and valik argument parsing
#87
eaasna
closed
1 year ago
1
Merge or split long sequences into technical bins
#86
eaasna
closed
1 year ago
1
Read reference metadata
#85
eaasna
closed
1 year ago
0
fix: return status in external_process is now parsed correctly
#84
SGSSGene
closed
1 year ago
0
fix: allow bin size 1
#83
SGSSGene
closed
1 year ago
0
[INFRA] measure external process time
#82
eaasna
closed
1 year ago
0
fix: updating badges url format and changing them to 'main'
#81
SGSSGene
closed
1 year ago
0
fix: ci workflows refere to main instead of master
#80
SGSSGene
closed
1 year ago
0
doc: adjusting the README to new parameters
#79
SGSSGene
closed
1 year ago
1
fix: return error code on failed search
#78
SGSSGene
closed
1 year ago
2
[INFRA] measure DREAM-Stellar search time
#77
eaasna
closed
1 year ago
0
[FEAT] Call parallel instances of Stellar search
#76
eaasna
closed
1 year ago
0
[FEAT] Create thread to call stellar as an external process
#75
eaasna
closed
1 year ago
1
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