This repository contains a workflow for phylogenetic placement and diversity analysis using QIIME 2 and external tools. The workflow integrates QIIME 2's standard analysis pipeline with custom steps for using external reference phylogenies, such as those created by the BACTRIA pipeline.
Key features:
- Integration of external reference phylogenies into QIIME 2 workflow
- Custom sequence placement
- Calculation of phylogenetic diversity metrics based on placements
- Scalable analysis for large metabarcoding datasets
This workflow uses Conda for dependency management. To set up the environment:
-
Clone this repository:
git clone https://github.com/yourusername/qiime2-phylogenetic-placement.git cd qiime2-phylogenetic-placement -
Create and activate the Conda environment:
conda env create -f workflow/envs/environment.yml conda activate qiime2-phylo-placement
The workflow is managed using Snakemake. To run the entire pipeline:
NOT YET IMPLEMENTED
Adjust the config/config.yaml file to set parameters for your analysis, including:
- Input data locations
- Reference phylogeny file
- QIIME 2 parameters
- Diversity metric calculations
Output files will be generated in the results/ directory, including:
- QIIME 2 artifacts
- Phylogenetic placements
- Diversity metric calculations