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jts
/
ncov-tools
Small collection of tools for performing quality control on coronavirus sequencing data and genomes
MIT License
47
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16
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Fix/metadata na
#111
rdeborja
closed
3 months ago
1
KeyError in `format_pileup.py`
#110
dfornika
opened
6 months ago
3
Check for empty merged dataframe before plotting
#109
dfornika
opened
6 months ago
0
Plotting scripts may crash if no metadata (Ct values) available
#108
dfornika
opened
6 months ago
9
Fix bug for primer prefixes containing numbers
#107
fmaguire
closed
1 year ago
0
Amplicon coverage heatmap plot
#106
AnyaKovalenko
closed
1 year ago
2
Where is the primers_to_amplicons.py script?
#105
juliadouglasf
closed
1 year ago
6
Pr 103
#104
rdeborja
closed
1 year ago
0
Add pangolin analysis mode option
#103
DarianHole
closed
1 year ago
1
Error: <Workflow defines configfile config.yaml but it is not present or accessible.>
#102
AnyaKovalenko
closed
2 years ago
4
ncov_tools bad interpreter: Permission denied error
#101
dgaston
closed
1 year ago
12
1.9 rc
#100
rdeborja
closed
2 years ago
0
Update conda environment for Pangolin v4.0+
#99
jaleezyy
closed
2 years ago
0
added sample names into ambiguous position report
#98
jpalmer37
closed
2 years ago
1
Question about ambiguity threshold
#97
ChadFibke
closed
2 years ago
5
forcing snakemake version to address TypeError
#96
rdeborja
closed
2 years ago
1
Create alleles file from VCF, generate SNP tree from new alleles VCF file
#95
rdeborja
opened
2 years ago
0
TypeError when running most recent Pangolin
#94
jpalmer37
closed
1 year ago
2
Remove config amplicon prefix when creating negative control report
#93
fmaguire
closed
3 years ago
0
Missing amplicon ID error
#92
dnhare
closed
3 years ago
6
Add reference indexing, support different primer name prefixes
#91
rdeborja
closed
3 years ago
1
pangolin error
#90
danieljbridges
closed
3 years ago
6
Create alleles from vcf
#89
rdeborja
closed
2 years ago
0
validate negative controls before reporting them
#88
rdeborja
closed
3 years ago
0
added pango-designation package to conda environment
#87
rdeborja
closed
3 years ago
0
Add B.1.617.2 to default VOC lineages
#86
fmaguire
closed
3 years ago
0
Lineage assignment of 'none' when processing many samples
#85
Mach-2
closed
3 years ago
13
fixed Flagged Samples Pangolin Notes column width
#84
rdeborja
closed
3 years ago
0
fixed column error from scorpio_call addition
#83
rdeborja
closed
3 years ago
0
Test pangolin 3
#82
rdeborja
closed
3 years ago
0
added creation of primer snp depth summary as part of all rule
#81
rdeborja
closed
3 years ago
0
Add configurable optional output directory
#80
fmaguire
closed
3 years ago
1
Improve VOC report
#79
jts
closed
3 years ago
0
build snpeff database at installation not run time.
#78
poquirion
opened
3 years ago
3
implement methods to identify variants that disrupt amplicons
#77
jts
closed
3 years ago
0
Add amplicon cov boxplot
#76
rdeborja
closed
3 years ago
0
snpEff database build support for different version
#75
rdeborja
closed
3 years ago
0
Issue building SnpEFF database
#74
DarianHole
closed
3 years ago
5
added -noLog option to snpEff
#73
rdeborja
closed
3 years ago
0
handle VOC sublineages
#72
jts
closed
3 years ago
1
Fix ct plots
#71
rdeborja
closed
3 years ago
0
Pangolin v2.3.0 now requires gofasta
#70
DarianHole
closed
3 years ago
1
PDF reports fails to generate due to missing "lineage_notes" key
#69
DarianHole
closed
3 years ago
2
Use action to publish docker image
#68
poquirion
closed
3 years ago
0
removed hardcoded file pattern reference
#67
rdeborja
closed
3 years ago
0
removed -lv flag from pangolin which has been deprecated
#66
rdeborja
closed
3 years ago
0
pangolin no longer has '-lv' flag
#65
dfornika
closed
3 years ago
1
Latest pangolin release breaks ncov-tools
#64
will-rowe
closed
3 years ago
4
Keep pangolin up to date automatically
#63
fmaguire
opened
3 years ago
1
Identifying amplicon dropouts
#62
rdeborja
closed
3 years ago
1
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