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bacpop
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ska.rust
Split k-mer analysis – version 2
https://docs.rs/ska/latest/ska/
Apache License 2.0
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Simplified proportion reads computation
#75
apollis44
closed
1 month ago
1
Adding max frequence reads parameter
#74
apollis44
closed
2 months ago
1
Adding max reads parameter
#73
apollis44
closed
2 months ago
1
Testing on a subsample of reads
#72
apollis44
closed
2 months ago
1
Add files via upload
#71
apollis44
closed
2 months ago
0
Consistent method for dealing with ref bias in ska map
#70
johnlees
closed
3 months ago
1
different results from ska2 0.3.2 and 0.3.6
#69
danrlu
opened
3 months ago
2
How do I cite this package?
#68
danrlu
closed
3 months ago
4
nanopore data
#67
PWSmit
opened
4 months ago
2
Fix double file prefix; update VCF parsing
#66
johnlees
closed
4 months ago
1
Suggestion: ska map to only report positions of variable split-kmers
#65
rderelle
closed
4 months ago
7
Suggestion: consistent output suffixes in ska weed
#64
rderelle
closed
4 months ago
1
Filter tweaks
#63
johnlees
closed
7 months ago
1
Defaults and filtering tweaks
#62
johnlees
closed
7 months ago
0
0.3.4 candidate -- final feature requests
#61
johnlees
closed
8 months ago
1
Fix for multi-contig references in map
#60
johnlees
closed
8 months ago
1
`ska map` fails with some fragmented reference sequences
#59
tmaklin
closed
8 months ago
3
Fix for ska delete
#58
johnlees
closed
9 months ago
1
ska merge and delete not working
#57
rderelle
closed
9 months ago
6
strange behaviour for min-count (ska build)
#56
rderelle
closed
8 months ago
9
Add optional output filename option `-o` to `ska weed`.
#55
tmaklin
closed
9 months ago
3
request: Iterator trait for MergeSkaArray
#54
rderelle
closed
8 months ago
1
Change middle base default filter to strict
#53
johnlees
closed
8 months ago
0
Possible changes to fastq input
#52
johnlees
opened
10 months ago
8
Feature request: filter out missing bases in ska align
#51
rderelle
closed
8 months ago
3
Feature requests: different mixture model; combined ska build & cov
#50
rderelle
opened
11 months ago
2
Fix for multicopy palindromes
#49
johnlees
closed
11 months ago
1
'Palindrome middle base not W/S: 78' in ska build
#48
jvfe
closed
11 months ago
6
Alternatives for .skf format
#47
johnlees
opened
11 months ago
4
Restore filter accuracy for fastq input
#46
johnlees
closed
11 months ago
0
Degraded performance of k-mer filter from FASTQ files
#45
johnlees
closed
11 months ago
14
Enchanced filtering options
#44
johnlees
closed
12 months ago
1
Documentation improvements
#43
johnlees
closed
12 months ago
0
Add filter to ska map, and ambiguous filter to ska weed
#42
johnlees
closed
12 months ago
1
Non-nucleotide bases produced within ska map alignment
#41
jdaeth274
closed
12 months ago
6
Add k-mer counts per sample to ska nk; efficiency of dup counting
#40
johnlees
closed
1 year ago
1
Add kmer count per sample to ska nk output
#39
danrlu
closed
10 months ago
7
The distance result is very different from the old version
#38
danrlu
closed
1 year ago
6
Mask repeats with Ns during ska map
#37
johnlees
closed
1 year ago
1
Add NJ trees to clustering script
#36
johnlees
closed
1 year ago
1
Add ska distance, and clustering script
#35
johnlees
closed
1 year ago
1
Add mode to automatically determine a count cutoff
#34
johnlees
closed
1 year ago
1
Fix filtering option name in documentation.
#33
tmaklin
closed
1 year ago
1
Add option for repeat mapping
#32
johnlees
closed
1 year ago
0
Fix ambiguous bases in pseudoalignment
#31
johnlees
closed
1 year ago
1
Deal with palindromes
#30
johnlees
closed
1 year ago
1
Add automatic coverage determination
#29
johnlees
closed
1 year ago
0
Reference bias in map with repeats
#28
johnlees
closed
1 year ago
0
Consider palindromic self-rc k-mers
#27
johnlees
closed
1 year ago
0
Add ska distance
#26
johnlees
closed
1 year ago
2
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