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theiagen
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public_health_viral_genomics
Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2
https://public-health-viral-genomics-theiagen.readthedocs.io/
GNU Affero General Public License v3.0
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Floating NextClade SC2 lineage calls to output table
#176
kevinlibuit
opened
2 years ago
0
VADR updates for MPXV; update default nextclade_dataset_tag and docker
#175
kapsakcj
closed
1 year ago
0
Adds VADR task and outputs for MPXV
#174
kapsakcj
closed
2 years ago
2
Mercury_Prep_N_Batch
#173
kevinlibuit
closed
1 year ago
0
citation.cff update
#172
kapsakcj
closed
2 years ago
1
New VADR output: `.zip` of output fasta files
#171
kapsakcj
closed
1 year ago
2
pull1
#170
PHemarajata
closed
2 years ago
0
Freyja Small Changes
#169
michellescribner
closed
1 year ago
0
TheiaCoV_Illumina_* if MPXV reference is not found, will use SC2 rather than error
#168
michellescribner
opened
2 years ago
0
iVar amino acid data not outputted
#167
michellescribner
opened
2 years ago
0
fix genome length calc
#166
sage-wright
closed
2 years ago
0
Capture reads from alignment
#165
kevinlibuit
closed
2 years ago
0
Capture Freyja Versions
#164
kevinlibuit
closed
2 years ago
0
Pangolin_Update change
#163
sage-wright
closed
1 year ago
1
Adds expanded to update
#162
sage-wright
closed
2 years ago
0
Update versions
#161
sage-wright
closed
2 years ago
0
Freyja Updates
#160
kevinlibuit
closed
2 years ago
1
Reorganize PHVG for MPXV
#159
sage-wright
closed
2 years ago
0
add miniwdl check workflow
#158
rpetit3
closed
2 years ago
2
Add expanded-lineage output to pangolin4 task and associated workflows
#157
kevinlibuit
closed
2 years ago
4
Update TheiaCoV workflows to utilize nextclade v2
#156
kevinlibuit
closed
2 years ago
1
Update to Nextclade v2
#155
kevinlibuit
closed
2 years ago
1
PHVG Read The Docs update
#154
emmadoughty
closed
2 years ago
1
Gisaid assembly files produced for empty consensus fastas
#153
michellescribner
opened
2 years ago
0
Capture of extended pango lineage
#152
kevinlibuit
closed
2 years ago
1
s-gene inputs as workflow attributes to ease user modification
#151
kevinlibuit
closed
2 years ago
0
Add pol region coverage stat to HIVGC
#150
frankambrosio3
closed
2 years ago
0
consensus_qc task not compatible with lowercase seqs in FASTAs
#149
kapsakcj
opened
2 years ago
0
In hivgc remove s gene coverage and implement pol region coverage
#148
frankambrosio3
closed
1 year ago
0
Add SIERRA to HIVGC
#147
frankambrosio3
closed
1 year ago
0
Adding alternative reference schemes for C-HIV
#146
frankambrosio3
closed
1 year ago
0
Adding Illumina version of HIV-GC workflow
#145
frankambrosio3
closed
1 year ago
2
Refactoring task files in the hiv-gc dev branch
#144
frankambrosio3
closed
1 year ago
1
Update ReadTheDocs
#143
kevinlibuit
closed
2 years ago
2
Mercury Prep variable type parsing
#142
sage-wright
closed
1 year ago
2
Fix PHVG v2.1.1 bug and update default images and tags
#141
sage-wright
closed
2 years ago
0
Updated version
#140
sage-wright
closed
2 years ago
0
Enables --skip-scorpio functionality
#139
sage-wright
closed
2 years ago
0
Comma-separated author list causes Augur_Run to fail
#138
sage-wright
closed
2 years ago
0
Smw fix mem dev
#137
sage-wright
closed
2 years ago
2
Issue with Medaka SC2 frameshifts and GISAID/GenBank rejections
#136
kevinlibuit
opened
2 years ago
1
Adding TheiaCoV_FASTA and Augur workflows
#135
kevinlibuit
opened
2 years ago
0
Update task_versioning.wdl
#134
kevinlibuit
closed
2 years ago
0
Capture Freyja docker
#133
sage-wright
closed
1 year ago
0
updat default pangolin docker image to 4.0.4
#132
kapsakcj
closed
2 years ago
0
Cjk pangolin v4 dev
#131
kapsakcj
closed
2 years ago
0
Update to Freyja v1.3.4
#130
kevinlibuit
closed
2 years ago
0
s_gene_percent_coverage float and percent_gene_coverage file for ClearLabs and ONT
#129
kapsakcj
closed
2 years ago
2
pangolin v4 & updating nextclade defaults across 6 workflows
#128
kapsakcj
closed
2 years ago
4
Various patches
#127
kevinlibuit
closed
2 years ago
0
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