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poreCov
SARS-CoV-2 workflow for nanopore sequence data
https://case-group.github.io/
GNU General Public License v3.0
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local config
#76
iferres
closed
3 years ago
5
Update president #72
#75
hoelzer
closed
3 years ago
3
Report style tweaks
#74
RaverJay
closed
3 years ago
9
Include unclassified in kraken2 stats
#73
RaverJay
closed
3 years ago
4
Update consensus QC
#72
hoelzer
closed
3 years ago
3
Adjust percentage of classified reads
#71
hoelzer
closed
3 years ago
1
bugfix for row swap, safe column adding
#70
RaverJay
closed
3 years ago
3
collect consensus sequences in one folder
#69
oliverdrechsel
closed
3 years ago
6
Report updates
#68
RaverJay
closed
3 years ago
3
clean up unpacked database
#67
RaverJay
closed
3 years ago
1
Report percentage of Ns
#66
hoelzer
closed
3 years ago
5
Report also Nextstrain INDEL positions
#65
hoelzer
closed
3 years ago
5
update pangolin
#64
hoelzer
closed
3 years ago
1
Add reference genome coverage to the report
#63
hoelzer
closed
3 years ago
3
Add absolute classification numbers to the report
#62
hoelzer
closed
3 years ago
0
Fix empty mutations + new fastdov version
#61
RaverJay
closed
3 years ago
1
Update guppy.nf
#60
replikation
closed
3 years ago
16
Clean-up
#59
hoelzer
closed
3 years ago
13
Optimize execution: multithreading, other tools, memory
#58
RaverJay
closed
3 years ago
2
Multithreaded bwa mem
#57
RaverJay
closed
3 years ago
1
Collate coverage plots to groups of 6 samples
#56
RaverJay
closed
3 years ago
1
Fixes summary report for new president version
#55
RaverJay
closed
3 years ago
0
Dev guppy adjust
#54
replikation
closed
3 years ago
1
Add multifasta support
#53
RaverJay
closed
3 years ago
0
replace rki csv
#52
replikation
closed
3 years ago
0
Summary report
#51
RaverJay
closed
3 years ago
11
Keep alignment file
#50
hoelzer
closed
3 years ago
3
up president, krakendb
#49
hoelzer
closed
3 years ago
1
Dev mutation to db
#48
replikation
closed
3 years ago
2
fix toInteger calls
#47
RaverJay
closed
3 years ago
0
Dev read classification
#46
replikation
closed
3 years ago
1
Gpu cloud
#45
replikation
closed
3 years ago
0
fixed quotation & added if-exclusion in json_parser
#44
DataSpott
closed
3 years ago
0
pangolin version tag
#43
replikation
closed
3 years ago
0
Ukj flag test
#42
DataSpott
closed
3 years ago
0
Ukj flag test
#41
DataSpott
closed
3 years ago
0
Dev ukj flag
#40
replikation
closed
3 years ago
0
Centrifuge for human host contamination
#39
replikation
closed
3 years ago
2
Mask coverage region parameterization
#38
replikation
closed
3 years ago
1
Readme
#37
replikation
closed
3 years ago
0
Publish basecalled FASTQ files
#36
hoelzer
closed
3 years ago
3
Filter FASTQ by length - report
#35
hoelzer
closed
3 years ago
3
flag for guppy singularity
#34
hoelzer
closed
3 years ago
0
Update guppy
#33
hoelzer
closed
3 years ago
4
Dev replikation
#32
replikation
closed
3 years ago
1
Only add genomes to final RKI FASTA and report.csv that meet QC criteria
#31
hoelzer
closed
3 years ago
6
ukj-Flag to create mongoDB database entry and "filename support"
#30
DataSpott
closed
3 years ago
1
Nextclade assignment
#29
hoelzer
closed
3 years ago
1
rki output and some smaller fixes
#28
replikation
closed
3 years ago
11
rki conform metadata output
#27
replikation
closed
3 years ago
2
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