Characterizing the Aerobiome
This repository acts as a centralized place where to store and display analyses of metagenomics (and other) analyses and characterization of the aerobiome.
Reproducibility
To reproduce the results shown in the reports, an working installation of conda to reproduce the environment is the easiest way to achieve this. To do so, please follow the steps below:
- Clone the repository
- Navigate to the root folder and run
conda env create -f environment.yml - You should be ready to go!
In case the environment creation fails, please check the environment.yml file and make sure that the packages are available for your platform.
Reports
The reports are generated using Jupyter Notebooks, mixing Markdown and Python code, with Quarto as the final renderer. Each report focuses on different aspects of aerobiome analysis:
Available Reports
| Report | Description | View Report |
|---|---|---|
| All Aerobiome Samples | Comprehensive analysis of all aerobiome samples collected | View Report |
| Kumamoto PacBio Analysis | PacBio sequencing data analysis from Kumamoto samples | View Report |
| NOTO Sampling Evaluation | Evaluation of sampling methods and protocols at NOTO station | View Report |
| NOTO Subdaily Analysis | High-resolution temporal analysis of aerobiome at NOTO | View Report |
| PacBio assemblies vs direct assignments | Comparison of assemblies vs direct assignments | View Report |