neherlab ncov-simple issues

neherlab / ncov-simple

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issues

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BUG: Not masking terminals?

#35 corneliusroemer opened 2 years ago
0
Filter out env samples

#34 corneliusroemer opened 3 years ago
0
Unmask S:95

#33 corneliusroemer closed 3 years ago
0
Add only internal Spike muts to branch label to reduce noise and focus on important ones

#32 corneliusroemer closed 3 years ago
0
TypeError in add_branch_labels.py

#31 corneliusroemer closed 3 years ago
0
Consider not hard masking S:95

#30 corneliusroemer closed 3 years ago
1
fix: add aa reference sequence back after switch to nextalign translation

#29 corneliusroemer closed 3 years ago
1
Amino acid sequences missing from root sequence, they used to be there

#28 corneliusroemer closed 3 years ago
0
feat: surface reconstructed insertions

#27 corneliusroemer closed 3 years ago
0
feat: reconstruct emergence of insertions and place on tree as branch labels

#26 corneliusroemer closed 3 years ago
4
explicit_translation.py local only: `AttributeError: 'NoneType' object has no attribute 'find'`

#25 corneliusroemer closed 3 years ago
5
feat: alternative masking scheme

#24 rneher closed 3 years ago
7
Use prealignment from ncov-ingest, save computation time

#23 corneliusroemer opened 3 years ago
5
Give samples with quick sampling->submission a relaxed upper clock filter limit, tighten upper limit otherwise

#22 corneliusroemer opened 3 years ago
0
feat: improved diagnostic, output reasons

#21 corneliusroemer closed 3 years ago
2
Private mutation counts are very high ~30 for regional lineages in countries that don't submit to Genbank

#20 corneliusroemer opened 3 years ago
0
Integrate clade_emergence filtering into diagnostic.py and workflow

#19 corneliusroemer closed 3 years ago
0
Add clock_deviation, rare mutations and other QC as colorings to help tune diagnostic.py cutoffs

#18 corneliusroemer opened 3 years ago
0
Switch off prioritisation for continents/global but keep for countries

#17 corneliusroemer opened 3 years ago
0
Better logging of diagnostic.py to help figure out reasons for exclusion

#16 corneliusroemer closed 3 years ago
0
Pango build for Nextclade

#15 corneliusroemer opened 3 years ago
3
Build tree with only pango designated sequences for Nextclade pango assignments

#14 corneliusroemer opened 3 years ago
0
Why is nuc:7851T (AY.4 defining) such a mess on the Europe tree?

#13 corneliusroemer opened 3 years ago
3
How did a Delta from 2020-07 make it past diagnostic.py?

#12 corneliusroemer closed 3 years ago
2
feat: use hard masked sequences for distance colorings

#11 corneliusroemer closed 3 years ago
1
feat: mask_hard

#10 corneliusroemer closed 3 years ago
1
Feat/mutational fitness

#9 corneliusroemer closed 3 years ago
0
Add mutational fitness

#8 corneliusroemer closed 3 years ago
0
Make distances more robust by masking S:95/142

#7 corneliusroemer closed 3 years ago
2
Hard masking of S:142 and S:95 to prevent artefactual ladderization

#6 corneliusroemer closed 3 years ago
0
Add insertions/frameshifts as branch labels

#5 corneliusroemer closed 3 years ago
2
Convert to Nextalign translation

#4 corneliusroemer closed 3 years ago
0
Feat/pango

#3 corneliusroemer closed 3 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