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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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Update Mercury Prep and Mercury Batch workflows to generate output compatible with GISAID's v4 command line uploader
#226
erikwolfsohn
opened
7 months ago
0
Update readme
#225
sage-wright
closed
1 year ago
0
update readme
#224
sage-wright
closed
1 year ago
0
update checksums
#223
sage-wright
closed
1 year ago
0
Add "consortium" to Mercury_Prep
#222
sage-wright
closed
1 year ago
1
wf_ivar_consensus obscures min_freq option
#221
michellescribner
closed
1 year ago
0
Add intermediate frequency mutations screen TheiaCoV
#220
michellescribner
closed
1 year ago
1
Mercury Fix when collection_date is missing
#219
sage-wright
closed
1 year ago
0
Update README.md
#218
kevinlibuit
closed
1 year ago
0
update default pangolin docker to staphb/pangolin:4.2-pdata-1.18.1.1 and nextclade_dataset_tag for SC2
#217
kapsakcj
closed
1 year ago
2
Fix Bug RE Type-B subtyping (TheiaCoV_Illumina PE flu track)
#216
kevinlibuit
closed
1 year ago
0
update github actions workflow
#215
kapsakcj
closed
1 year ago
6
Add detection for aa substitutions associated with tamiflu-resistance
#214
cimendes
closed
1 year ago
0
update nextclade TSV parsing for SC2: `clade_legacy`. Also update Flu & nextclade
#213
kapsakcj
closed
1 year ago
6
nextclade parsing changes into stable dev branch
#212
kapsakcj
closed
1 year ago
2
Expose minimum coverage option in Freyja_Plot
#211
sage-wright
closed
1 year ago
0
Enable alternative read and assembly files
#210
sage-wright
closed
1 year ago
2
Mercury_Prep_N_Batch: make state input variable optional
#209
sage-wright
closed
1 year ago
0
Add mincov to Freyja_Plot
#208
sage-wright
closed
1 year ago
0
Enable alternative read and assembly files
#207
sage-wright
closed
1 year ago
1
Mercury_Prep_N_Batch: fixes
#206
sage-wright
closed
1 year ago
1
Smw excluded mercury dev
#205
sage-wright
closed
1 year ago
0
quality exclusion write out
#204
sage-wright
closed
1 year ago
0
Update version and SC2 references
#203
kevinlibuit
closed
1 year ago
1
Ensure bbduk outputs are ordered
#202
kevinlibuit
closed
1 year ago
0
Fix lowercase things
#201
sage-wright
closed
1 year ago
0
IRMA fails with too many reads
#200
frankambrosio3
opened
1 year ago
2
Fix conditional logic in Mercury Prep N Batch
#199
sage-wright
closed
1 year ago
0
Fja hiv merge dev
#198
frankambrosio3
closed
1 year ago
1
Pangolin_Update redundant output variable
#197
sage-wright
closed
1 year ago
0
the Mercury_Prep_N_Batch workflow
#196
sage-wright
closed
1 year ago
1
TheiaCov output - Nextclade_lineage empty
#195
kapsakcj
closed
1 year ago
0
Adding flu organism track
#194
kevinlibuit
closed
1 year ago
1
Azure compatibility
#193
sage-wright
closed
1 year ago
0
Implement workflow logic to use "mpox" as the target organism for TheiaCoV MPXV analysis
#192
frankambrosio3
opened
1 year ago
0
Add organism track for flu characterization
#191
kevinlibuit
closed
1 year ago
1
adds support for running VADR on WNV samples
#190
kapsakcj
closed
1 year ago
0
Make pipelines azure comaptible.
#189
vsmalladi
closed
1 year ago
4
link to the notion page in 2.2.0
#188
neranjan007
opened
1 year ago
1
ensure WDL compatibility with Azure
#187
vsmalladi
closed
1 year ago
2
Rp3 add support for adapter files in bbduk, update ci test
#186
kapsakcj
closed
1 year ago
0
add support for adapter files in bbduk, update ci test
#185
rpetit3
closed
1 year ago
2
allow user to specify adapters FASTA for trimming with bbduk
#184
kapsakcj
closed
1 year ago
0
fastq-scan fails on large FASTQs
#183
kapsakcj
opened
1 year ago
2
Add optional arguments input to trimmomatic task and add fastp task
#182
michellescribner
closed
1 year ago
0
Fja merc dev
#181
frankambrosio3
closed
1 year ago
0
VADR for WNV
#180
kevinlibuit
closed
1 year ago
2
VADR for MPXV
#179
kevinlibuit
closed
1 year ago
1
Aviti compatibility
#178
kevinlibuit
closed
1 year ago
1
Add fastp option to TheiaCoV_Illumina_* workflows
#177
michellescribner
closed
1 year ago
1
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