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mbhall88
/
tbpore
Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
MIT License
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2
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chore(main): release 0.7.1
#58
github-actions[bot]
closed
3 months ago
1
fix: update rasusa usage for latest version
#57
mbhall88
closed
3 months ago
1
TBpore fails while running rasusa
#56
ycode-sh
closed
3 months ago
8
chore(main): release 0.7.1
#55
github-actions[bot]
closed
11 months ago
1
chore(main): release 0.7.0
#54
github-actions[bot]
closed
11 months ago
1
Expose subsampling options
#53
mbhall88
closed
11 months ago
1
Add option for strongly connected components
#52
mbhall88
closed
11 months ago
1
Add mapping reads stats
#51
mbhall88
closed
1 year ago
0
Add stats
#50
mbhall88
closed
1 year ago
0
Subsampled meaning
#49
jloubser
closed
1 year ago
3
Sort fastq to ensure reproducibility
#48
mbhall88
closed
1 year ago
0
Better handling of decontamination database
#47
mbhall88
closed
1 year ago
1
Remove only fastq extension
#46
mbhall88
closed
1 year ago
1
Error calling samtools (return code 1)
#45
FlorianePoint
closed
1 year ago
4
Add cache directory option
#44
mbhall88
closed
1 year ago
1
Singularity Container read-only file system error
#43
pedrodcb
closed
1 year ago
6
Add option to set decontamination database index path
#42
mbhall88
closed
1 year ago
3
Update README to refer to the decontamination index from figshare and other README updates
#41
leoisl
closed
2 years ago
3
Comparing paper results with results with new filters (min_depth 5, min_qual 25, min_mq 30)
#40
leoisl
closed
1 year ago
14
add release workflow
#39
mbhall88
closed
2 years ago
1
Investigate `just test-run` not working
#38
leoisl
closed
1 year ago
7
Run several samples at once
#37
leoisl
closed
1 year ago
4
Build a tree from clustering
#36
leoisl
closed
1 year ago
12
Make the reference configurable
#35
leoisl
opened
2 years ago
10
Switch away from conda
#34
leoisl
closed
1 year ago
15
Move decontamination DB index to zenodo
#33
leoisl
closed
2 years ago
0
Add conda recipe and release v0.1.0
#32
leoisl
closed
2 years ago
0
Test the impact on clustering of changing `minimap2` index to use less RAM
#31
leoisl
opened
2 years ago
3
Improve README.md
#30
leoisl
closed
2 years ago
1
Adds subcommand `tbpore cluster`
#29
leoisl
closed
2 years ago
2
Add flag to make decontamination optional?
#28
leoisl
closed
2 years ago
2
Check md5sum or sha256 of decontamination DB index to ensure we have the correct index
#27
leoisl
closed
2 years ago
3
Adding decontamination and a few other misc stuff
#26
leoisl
closed
2 years ago
1
Create subcommand `tbpore cluster`
#25
leoisl
closed
2 years ago
15
Add minimap2 index URL
#24
leoisl
closed
2 years ago
0
Comparing `H2H` and `tbpore` output step by step
#23
leoisl
closed
2 years ago
7
Threshold for the phred-scaled VCF call quality
#22
leoisl
closed
2 years ago
19
Remove contamination
#21
leoisl
closed
2 years ago
1
Decontamination has a huge effect on real data tests
#20
leoisl
closed
2 years ago
27
Performance
#19
leoisl
closed
2 years ago
4
Duplicated files input bug
#18
leoisl
closed
2 years ago
0
Directory input bug
#17
leoisl
closed
2 years ago
2
Real data test, tbpore vs head-to-head pipeline
#16
leoisl
closed
2 years ago
66
Check H37RV data
#15
leoisl
closed
2 years ago
1
Add sample example
#14
leoisl
closed
2 years ago
4
Update README.md
#13
leoisl
closed
2 years ago
0
Cryptic Mac OS CI issue
#12
leoisl
closed
2 years ago
4
Linting
#11
leoisl
closed
2 years ago
1
Output directory param or output consensus param?
#10
leoisl
closed
2 years ago
5
Cache mykrobe/ctx binary skeletons
#9
leoisl
closed
2 years ago
2
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