Comments (1)
It is not recommended to use MOB-recon on metagenomics since a key assumption it makes is that there is only one version of a mob-cluster present. This would likely cause plasmids which have multiple versions assembling of the MOB-cluster failing to get classified or a jumbled mess of contigs. You can definitely use MOB-typer on the reconstructed contigs you get from another software. We are contemplating extending functionality for plasmids in metagenomes but that is not something we have the resources to work on at present.
from mob-suite.
Related Issues (20)
- Conda instalation fails HOT 3
- Coverage threshold not applied for tblastn searches HOT 2
- Feature suggestion: Confirm plasmids from assembly graphs
- hostrange() missing 1 required positional argument: 'database_directory' HOT 1
- mob_typer -d with not-yet-initialized db path fails HOT 3
- Feature request: Support `circular=Y` for detecting circularized contigs
- MOB-recon v3.1.7 fails at the biomarker stage. HOT 3
- Mob_Recon fails with compressed input HOT 1
- Pandas version issue when installing using conda/mamba HOT 2
- mob_recon's error: "TypeError: to_csv() got an unexpected keyword argument 'line_terminator'" HOT 5
- Command line to run batch of samples in mob_recon
- A circular contig with replicons from a hybrid assembly is classified as a chromosome
- mob_recon does not reconstruct plasmids sequences HOT 1
- Results depend on the ordering of the input fasta HOT 1
- mob_init fails HOT 1
- TypeError: hostrange() missing 1 required positional argument: 'database_directory' HOT 1
- Installation problem from conda HOT 7
- Cannot find mob-typer accessions on NCBI HOT 4
- Database not installed properly
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 mob-suite.