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neherlab
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ncov-simple
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BUG: Not masking terminals?
#35
corneliusroemer
opened
2 years ago
0
Filter out env samples
#34
corneliusroemer
opened
2 years ago
0
Unmask S:95
#33
corneliusroemer
closed
2 years ago
0
Add only internal Spike muts to branch label to reduce noise and focus on important ones
#32
corneliusroemer
closed
2 years ago
0
TypeError in add_branch_labels.py
#31
corneliusroemer
closed
2 years ago
0
Consider not hard masking S:95
#30
corneliusroemer
closed
2 years ago
1
fix: add aa reference sequence back after switch to nextalign translation
#29
corneliusroemer
closed
2 years ago
1
Amino acid sequences missing from root sequence, they used to be there
#28
corneliusroemer
closed
2 years ago
0
feat: surface reconstructed insertions
#27
corneliusroemer
closed
2 years ago
0
feat: reconstruct emergence of insertions and place on tree as branch labels
#26
corneliusroemer
closed
2 years ago
4
explicit_translation.py local only: `AttributeError: 'NoneType' object has no attribute 'find'`
#25
corneliusroemer
closed
2 years ago
5
feat: alternative masking scheme
#24
rneher
closed
2 years ago
7
Use prealignment from ncov-ingest, save computation time
#23
corneliusroemer
opened
2 years ago
5
Give samples with quick sampling->submission a relaxed upper clock filter limit, tighten upper limit otherwise
#22
corneliusroemer
opened
2 years ago
0
feat: improved diagnostic, output reasons
#21
corneliusroemer
closed
2 years ago
2
Private mutation counts are very high ~30 for regional lineages in countries that don't submit to Genbank
#20
corneliusroemer
opened
2 years ago
0
Integrate clade_emergence filtering into diagnostic.py and workflow
#19
corneliusroemer
closed
2 years ago
0
Add clock_deviation, rare mutations and other QC as colorings to help tune diagnostic.py cutoffs
#18
corneliusroemer
opened
2 years ago
0
Switch off prioritisation for continents/global but keep for countries
#17
corneliusroemer
opened
2 years ago
0
Better logging of diagnostic.py to help figure out reasons for exclusion
#16
corneliusroemer
closed
2 years ago
0
Pango build for Nextclade
#15
corneliusroemer
opened
2 years ago
3
Build tree with only pango designated sequences for Nextclade pango assignments
#14
corneliusroemer
opened
2 years ago
0
Why is nuc:7851T (AY.4 defining) such a mess on the Europe tree?
#13
corneliusroemer
opened
2 years ago
3
How did a Delta from 2020-07 make it past diagnostic.py?
#12
corneliusroemer
closed
2 years ago
2
feat: use hard masked sequences for distance colorings
#11
corneliusroemer
closed
2 years ago
1
feat: mask_hard
#10
corneliusroemer
closed
2 years ago
1
Feat/mutational fitness
#9
corneliusroemer
closed
2 years ago
0
Add mutational fitness
#8
corneliusroemer
closed
2 years ago
0
Make distances more robust by masking S:95/142
#7
corneliusroemer
closed
2 years ago
2
Hard masking of S:142 and S:95 to prevent artefactual ladderization
#6
corneliusroemer
closed
2 years ago
0
Add insertions/frameshifts as branch labels
#5
corneliusroemer
closed
2 years ago
2
Convert to Nextalign translation
#4
corneliusroemer
closed
2 years ago
0
Feat/pango
#3
corneliusroemer
closed
2 years ago
0
Combine swiss and country workflows into one
#2
corneliusroemer
closed
3 years ago
0
Modified .gitignore to exclude auspice-* and build-*
#1
corneliusroemer
closed
3 years ago
0