Comments (5)
Brilliant question.
Most people tend to exclude the plasmid from the phylogeny tree.
We can be smart and have two trees: one for the plasmid to show plasmid evolution and the other for the chromosome.
from ctgap.
We'll need a way to separate the plasmid sequence from the core genome of Ct.
Not sure how to handle this in the pipeline at this moment. There's a few options:
- Annotate everything, then parse out the contigs annotated with plasmid or similar - not sure how this will go because plasmid annotations could be unpredicatable
- blast for dnaA/repA to detect replication gene then pull out
- something else?
from ctgap.
The best way is BLAST and pull.
This is what I do manually anyway.
from ctgap.
What blastdb do you use?
from ctgap.
Sorry, I do my blast in genious without any db of mine.
I can curate a db and send it over tomorrow
from ctgap.
Related Issues (16)
- Changes for v0.02 HOT 7
- v0.3.0 HOT 7
- to-do HOT 1
- some quick fixes: HOT 1
- error: HOT 1
- add phylogeny output HOT 8
- Scrubby updates HOT 7
- reference 'guided' consensus assembly
- create plurality consensus from 24 reference genomes HOT 1
- rename outputs to sample name
- add dnaapler to reorientate contigs HOT 1
- automate ref-denovo for specific reference strain
- Add snippy for SNP detection HOT 3
- Add QUASt HOT 3
- Scrubby/fastp order HOT 6
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 ctgap.