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neherlab
/
ncov-simple
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neherlab/ncov-simple Issues
explicit_translation.py local only: `AttributeError: 'NoneType' object has no attribute 'find'`
Closed
3 years ago
Comments count
5
BUG: Not masking terminals?
Updated
3 years ago
Filter out env samples
Updated
3 years ago
Add only internal Spike muts to branch label to reduce noise and focus on important ones
Closed
3 years ago
Add insertions/frameshifts as branch labels
Closed
3 years ago
Comments count
2
Consider not hard masking S:95
Closed
3 years ago
Comments count
1
Unmask S:95
Closed
3 years ago
Make distances more robust by masking S:95/142
Closed
3 years ago
Comments count
2
TypeError in add_branch_labels.py
Closed
3 years ago
Amino acid sequences missing from root sequence, they used to be there
Closed
3 years ago
Better logging of diagnostic.py to help figure out reasons for exclusion
Closed
3 years ago
Integrate clade_emergence filtering into diagnostic.py and workflow
Closed
3 years ago
Use prealignment from ncov-ingest, save computation time
Updated
3 years ago
Comments count
5
Give samples with quick sampling->submission a relaxed upper clock filter limit, tighten upper limit otherwise
Updated
3 years ago
Private mutation counts are very high ~30 for regional lineages in countries that don't submit to Genbank
Updated
3 years ago
How did a Delta from 2020-07 make it past diagnostic.py?
Closed
3 years ago
Comments count
2
Add clock_deviation, rare mutations and other QC as colorings to help tune diagnostic.py cutoffs
Updated
3 years ago
Switch off prioritisation for continents/global but keep for countries
Updated
3 years ago
Build tree with only pango designated sequences for Nextclade pango assignments
Updated
3 years ago
Why is nuc:7851T (AY.4 defining) such a mess on the Europe tree?
Updated
3 years ago
Comments count
3
Hard masking of S:142 and S:95 to prevent artefactual ladderization
Closed
3 years ago
Add mutational fitness
Closed
3 years ago