ParaMAG: Pipeline for Metagenome-Assembled Genomes for Intracellular Parasites

This repository contains a Snakemake pipeline and a corresponding conda environment file for performing metagenomic assembly, binning, and phylogenomic analysis, with a focus on intracellular parasites and other organisms with reduced genomes.

Requirements

• Snakemake
• Python 3.8+
• Conda (optional, but recommended)

Installation

Clone this repository:

git clone https://github.com/mikeraiko/ParaMAG.git
cd ParaMAG

Usage

Step 1: Run with your own data

Prepare your input files and create a minimal config file config.yaml like this:

reads1: data/sample_R1.fastq.gz
reads2: data/sample_R2.fastq.gz
adapter_file: adapters/TruSeq3-PE.fa

Then run the wrapper script:

python paramag.py --run --config config.yaml

Step 2: Run on example data

To test the pipeline:

python paramag.py --example

This will automatically run the full workflow on a small test dataset.

Help

For help and additional options:

python paramag.py --help

Output

• maxbin_output/: binned genomes
• busco_output/: completeness metrics
• super_tree_output.tre: consensus tree
• report/summary_report.md: summary report