Comments (2)
I think this is due to the default behavior of augur translate
being to infer ambiguous nucleotides, and could be remedied by adding --keep-ambiguous
to the ancestral rule.
from avian-flu.
Thanks for flagging this! This is definitely an error caused by the combination of --fill-gaps
in augur align
and not having --keep-ambiguous
in augur translate
. This has been fixed with this commit, which does a few things:
- Removes
--fill-gaps
inaugur align
- Adds
--keep-ambiguous
inaugur translate
- Adds a new rule,
rule cleavage-site
, which reads in the HA alignment, translates it, and infers whether the 4 amino acids immediately preceding HA2 encode a furin cleavage motif. Here, I've defined a furin cleavage motif as the sequenceR-X-K/R-R
, whereX
is any amino acid. This results in 2 new colorby options:furin cleavage motif
, which can bepresent
orabsent
, andcleavage site sequence
, which displays the sequence of the 4 amino acids immediately preceding HA2.
As expected, we now display that some high-path H5N1 and H5Nx lineages have furin cleavage sites, but that the vast majority of H9N2 and H7N9 sequences do not.
from avian-flu.
Related Issues (20)
- Annotate H5 clades through a node data JSON file instead of modifying metadata
- Ingest Andersen Lab metadata and sequences HOT 6
- Ingest NCBI GenBank data for H5N1 outbreak HOT 7
- ingest: Upload NCBI/Andersen lab outputs to S3
- ingest: Join NCBI and Andersen lab data
- Automate ingest via GH Actions
- ingest: Run Nextclade as part of ingest HOT 2
- ingest/andersen-lab: Switch to automated CSV file HOT 1
- Add GH Action for phylogenetic workflows
- Reduce inference of unknown data/location for SRA sequences HOT 1
- ingest/ncbi: use new augur curate commands
- NCBI automation: connect ingest and phylogenetic workflows
- Snakemake improvements HOT 2
- Automated NCBI workflow not storing cache as expected
- NCBI/Andersen-lab: duplicate strain names HOT 3
- Adding USDA genotype and lineage
- Explore NCBI Assembly records to link segment sequences
- Not able to build / download data sets HOT 4
- Add `Snakefile.clades` rules into main snakefile
- Add fauna path to config HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from avian-flu.