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nextstrain
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WNV
the repository used to build West Nile Virus for nextstrain
https://nextstrain.org/WNV/NA
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Link out to Nextclade
#49
j23414
closed
1 hour ago
0
Add frequencies plot
#48
j23414
opened
1 day ago
0
Use IQ-Tree as the faster builder
#47
j23414
closed
1 day ago
1
Replace RAxML tree building with IQ-Tree
#46
j23414
closed
1 day ago
1
Enable multithreading to avoid 6hr time-out during github action
#45
j23414
closed
2 days ago
1
Ingest to phylogenetic workflow fails because job exceeds 6hrs
#44
joverlee521
closed
2 days ago
1
Add Nextclade extension
#43
j23414
closed
1 hour ago
5
Add "Host Genus" and "Host Type" coloring to the phylogenetic tree
#42
j23414
closed
4 days ago
1
Ingest: annotate EF631122 and EF631123 as unknown collection date
#41
j23414
closed
4 days ago
0
Ingest: fetch and append pathoplexus global lineage calls
#40
j23414
closed
1 week ago
4
Map host genus and host type
#39
DOH-LMT2303
closed
4 days ago
3
Fix molecular clock based on literature search
#38
j23414
closed
2 weeks ago
1
Updating to nextclade v3
#37
DOH-LMT2303
closed
3 weeks ago
0
Fix molecular clock in global tree
#36
j23414
closed
2 weeks ago
0
Perhaps append Pathoplexus WNV lineage calls
#35
j23414
closed
1 week ago
0
Use lineages for build targets
#34
trvrb
opened
4 weeks ago
0
Decide on reasonable min-length filter
#33
j23414
opened
1 month ago
1
Document decision points in the WNV phylogenetic build
#32
DOH-LMT2303
opened
1 month ago
0
Explicitly use Nextclade v3
#31
joverlee521
closed
3 weeks ago
0
Global tree and separating out the WA-specific configs
#30
j23414
closed
3 weeks ago
3
Annotation fixes
#29
j23414
closed
1 month ago
0
Add `is_lab_host` column to metadata
#28
j23414
closed
1 month ago
0
Preprocess host-species into a smaller list
#27
j23414
closed
4 days ago
1
Investigate a reasonable root for a global build
#26
j23414
closed
3 weeks ago
2
Restrict Nextclade assignments to NY99 and sub-branches, not across the global tree
#25
j23414
opened
1 month ago
1
Add color by mutation (versus color by Nextclade)
#24
j23414
opened
1 month ago
0
Fix cache
#23
joverlee521
closed
1 month ago
2
ingest/automation: Update S3 URLs to uppercase
#22
joverlee521
closed
1 month ago
1
Turn on clock feature
#21
j23414
closed
1 month ago
0
Separate out state-specific subsampling
#20
j23414
closed
3 weeks ago
1
Various fixes for the phylogenetic workflow automation
#19
j23414
closed
1 month ago
0
Refactor phylogenetic workflow to allow either ingest/results/locally_annotated_data or download open data from s3
#18
j23414
closed
3 weeks ago
1
Change the final auspice dataset name
#17
j23414
closed
1 month ago
0
Capitalization
#16
j23414
opened
1 month ago
0
Use vendored scripts instead of maintaining a separate copy
#15
j23414
closed
1 month ago
0
Add logs and benchmarks
#14
DOH-LMT2303
closed
1 month ago
0
Add automation for public build
#13
j23414
closed
1 month ago
0
Refactor phylogenetic such that a reasonable phylogenetic/build-configs/ci works
#12
j23414
closed
1 month ago
1
Add log and benchmarks to snakemake rules
#11
j23414
closed
1 month ago
0
Add description file
#10
j23414
closed
2 months ago
0
Add automated build workflows
#9
j23414
closed
1 month ago
0
Add custom description to Auspice dataset
#8
victorlin
closed
2 months ago
0
Use the latest "augur curate" commands and various other refactoring
#7
j23414
closed
3 months ago
0
ingest: use new augur curate commands
#6
j23414
closed
3 months ago
0
Development
#5
DOH-PNT0303
closed
6 months ago
1
Nextclade workflow for creating a dataset
#4
j23414
closed
5 months ago
1
Update the geolocation rules and lat long processing for NCBI datasets data
#3
j23414
closed
8 months ago
2
Document subsampling logic
#2
huddlej
closed
8 months ago
0
Add first attempt at generic subsampling
#1
huddlej
closed
9 months ago
1