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IKIM-Essen
/
uncovar
Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.
https://ikim-essen.github.io/uncovar
BSD 2-Clause "Simplified" License
20
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7
forks
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Add csv table in report of all kallisto calls
#517
thomasbtf
opened
2 years ago
0
chore(deps): bump github/super-linter from 4.9.0 to 4.9.1
#516
dependabot[bot]
closed
2 years ago
0
fix: primer clipping add up- and downstream
#515
alethomas
closed
2 years ago
0
generate report without found species diversity
#514
alethomas
opened
2 years ago
0
chore(fmt): update pre-commit deps
#513
thomasbtf
closed
2 years ago
2
chore(master): release 0.15.0
#512
github-actions[bot]
closed
2 years ago
1
chore(deps): bump peter-evans/create-pull-request from 3 to 4
#511
dependabot[bot]
closed
2 years ago
5
feat: update rbt to 0.39
#510
alethomas
closed
2 years ago
0
automatically generate folders for data handling
#509
alethomas
opened
2 years ago
0
newly initialized repo can't handle empty sample sheet
#508
alethomas
opened
2 years ago
0
feat: update snakemake version for resigned workflow
#507
thomasbtf
closed
5 months ago
3
Adjust structure of workflow for snakedeploy
#506
thomasbtf
opened
2 years ago
0
fix: add nofilter flag for variant calls
#505
thomasbtf
closed
2 years ago
0
Add more Illumina sequences to the CI environment
#504
thomasbtf
opened
2 years ago
0
chore: update copyright preamble
#503
github-actions[bot]
opened
2 years ago
0
Primer clipping
#502
thomasbtf
closed
2 years ago
1
ci: upload correct report
#501
thomasbtf
closed
2 years ago
0
ci: remove old primer files from test
#500
thomasbtf
closed
2 years ago
0
chore: update copyright preamble
#499
github-actions[bot]
closed
2 years ago
0
fix: reduce loading time of coverage plots
#498
thomasbtf
closed
2 years ago
0
Add a minimum percentage of SARS-CoV-2 in the sample as criteria to create a pseudo assembly
#497
thomasbtf
opened
2 years ago
0
Replace outdated df.append
#496
alethomas
closed
2 years ago
0
chore: update copyright preamble
#495
github-actions[bot]
closed
2 years ago
0
Make number of lineages configurable in VOC table
#494
alethomas
opened
2 years ago
0
docs(readme): remove author list
#493
thomasbtf
closed
2 years ago
0
feat: make sending lab column in rki report csv adjustable via config file
#492
lenakinzel
closed
2 years ago
0
fix: untemp recalibrated bam
#491
alethomas
closed
2 years ago
0
chore(deps): bump actions/setup-python from 2 to 3
#490
dependabot[bot]
closed
2 years ago
0
perf: Ont downsampling normalization
#489
simakro
closed
2 years ago
2
fix(ci): change human reference from NC_000021.9 to BA000005.3
#488
thomasbtf
closed
2 years ago
0
feat: add variant call details based on protein annotation
#487
thomasbtf
closed
2 years ago
0
Add CI check for VOC table
#486
alethomas
opened
2 years ago
0
Add variant overview plot
#485
thomasbtf
opened
2 years ago
1
fix: refactor VOC mutation table generation
#484
alethomas
closed
2 years ago
0
fix: pangolin plot
#483
alethomas
closed
2 years ago
0
Ability to identify the ORF1ab mutations as mutations of the individual functional proteins
#482
thomasbtf
closed
2 years ago
0
fix(ci): change release please PR branch
#481
thomasbtf
closed
2 years ago
0
fix: add index for vcf report
#480
alethomas
closed
2 years ago
0
feat: include lineage variant table for wastewater samples
#479
alethomas
closed
2 years ago
0
refactor(deps): update environment files
#478
thomasbtf
closed
2 years ago
2
fix(ci): release please checkout branch
#477
thomasbtf
closed
2 years ago
0
fix(ci): add missing missing echo to release please
#476
thomasbtf
closed
2 years ago
0
perf: add ont temp flags
#475
alethomas
closed
2 years ago
1
fix(ci): parse new json output from release please
#474
thomasbtf
closed
2 years ago
1
fix: canu and porechop porechop
#473
thomasbtf
closed
2 years ago
0
chore(deps): bump github/super-linter from 4.8.7 to 4.9.0
#472
dependabot[bot]
closed
2 years ago
4
To many Ns in final sequnces
#471
thomasbtf
opened
2 years ago
0
VOC similarity table
#470
thomasbtf
closed
2 years ago
1
MultiQC naming
#469
thomasbtf
opened
2 years ago
0
Reduced size of variants over time plot
#468
thomasbtf
opened
2 years ago
0
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