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Clinical-Genomics
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microSALT
Microbial Sequence Analysis and Loci-based Typing pipeline for use on NGS WGS data.
GNU General Public License v3.0
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Expanded testing. init now initializes logger, auto-creates directories
#82
sylvinite
closed
4 years ago
0
Fix percentage of ordered reads in QC-report
#81
talnor
closed
4 years ago
2
Added pytest and cleaned up example config
#80
sylvinite
closed
4 years ago
0
Resync function updates
#79
sylvinite
closed
4 years ago
0
Resync and contact updates
#78
sylvinite
closed
4 years ago
0
Stripping user input in response to issue
#77
sylvinite
closed
4 years ago
0
Additional typing definitions
#76
sylvinite
closed
8 months ago
0
HOTFIX: Improved fastq-file inclusion for analysis
#75
sylvinite
closed
5 years ago
1
install.sh update
#74
sylvinite
closed
5 years ago
0
Basic cgMLST implementation
#73
sylvinite
closed
8 months ago
0
Rerun flag reimplementation
#72
sylvinite
closed
5 years ago
0
Improved organism check
#71
sylvinite
closed
5 years ago
0
Auxillary Quality of Life
#70
sylvinite
closed
5 years ago
1
Stability for latest typing report
#69
sylvinite
closed
5 years ago
2
Replaced corner Novel with more informative status
#68
sylvinite
closed
5 years ago
0
Virology
#67
sylvinite
closed
5 years ago
0
Qc accreditation
#66
sylvinite
closed
5 years ago
0
Qc thresholds
#65
sylvinite
closed
5 years ago
0
Accreditation changes to report
#64
sylvinite
closed
5 years ago
2
Improved standards, take 1
#63
sylvinite
closed
5 years ago
0
Virulence definitions
#62
sylvinite
closed
5 years ago
0
Last second fixes
#61
sylvinite
closed
5 years ago
2
Report storage
#60
sylvinite
closed
5 years ago
1
Hasta integration
#59
sylvinite
closed
5 years ago
1
Uncareful
#58
sylvinite
closed
5 years ago
0
QC integration
#57
sylvinite
closed
5 years ago
0
Command line config, attempt 1
#56
sylvinite
closed
5 years ago
0
Attempted lint support
#55
sylvinite
closed
5 years ago
0
Syncing QC
#54
sylvinite
closed
5 years ago
0
QoL ST update, updates
#53
sylvinite
closed
5 years ago
0
Customer ID extraction
#52
sylvinite
closed
5 years ago
0
Internal
#51
sylvinite
closed
5 years ago
0
Woopsie on the json
#50
sylvinite
closed
5 years ago
0
Json report format
#49
sylvinite
closed
5 years ago
0
Changing of delivery reports 7.8.8 - saving of old results/reports
#48
emmser
closed
5 years ago
1
Freed post-cgMLST updates
#47
sylvinite
closed
5 years ago
0
Master sync to QC
#46
sylvinite
closed
5 years ago
0
Syncing dev to master
#45
sylvinite
closed
5 years ago
0
Change report to follow accreditation guidelines
#44
emmser
closed
5 years ago
3
Step 1 of ST establishment
#43
sylvinite
closed
5 years ago
1
Minor upgrades for testing
#42
sylvinite
closed
5 years ago
0
Resistance call debug info
#41
sylvinite
closed
4 years ago
0
Ta bort expanderad resistance Novel (allele)
#40
sylvinite
closed
5 years ago
1
Integration overview. Will be closed
#39
sylvinite
closed
5 years ago
0
cgMLST arbitary integration
#38
sylvinite
closed
5 years ago
0
Arbitary QC integration
#37
sylvinite
closed
5 years ago
0
Arbitary integration point.
#36
sylvinite
closed
5 years ago
0
CSV expansion
#35
sylvinite
closed
5 years ago
0
Config can be provided via CLI. CSV output format readded in util
#34
sylvinite
closed
5 years ago
0
Big project improvements and much more
#33
sylvinite
closed
5 years ago
0
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