Snakemake Ensemble Assembly Pipeline

This repository contains a bioinformatics pipeline for ensemble genome assembly using Snakemake. The pipeline integrates de novo and reference-based assembly approaches to improve assembly quality for similar (e.g., bacterial) genomes while removing contaminant sequences (e.g., from host DNA).

Project Structure

.
├── README.md              # This file
├── config                 # Configuration files
│   └── config.yaml        # Main configuration
├── resources              # Resources (e.g., reference genomes)
├── results                # Results directory
└── workflow               # Snakemake workflow
    ├── Snakefile          # Main Snakemake file
    ├── env                # Conda environments
    ├── rules              # Snakemake rules (e.g., assembly, filtering)
    └── scripts            # Auxiliary scripts

Installation

1. Create Conda environment:

   conda env create -f workflow/env/myenv.yaml
   conda activate myenv

2. Install Snakemake (if not already installed):

   conda install -c conda-forge snakemake

Running the Pipeline

To run the pipeline:

snakemake --use-conda

Configuration

Edit config/config.yaml to customize parameters such as input FASTQ files, reference genome path, and tool settings for the assembly steps.

Workflow Overview

• Initial de novo assembly of input reads
• Selection of best assembly to serve as reference
• Reference-based improvement of other assemblies
• Consensus genome construction
• Filtering of contaminant sequences

Results

Output files will be saved in the results/ directory and include assembled genomes, intermediate files, quality reports, and the final consensus assembly.

Acknowledgments

This pipeline incorporates tools for de novo and reference-based genome assembly. Tool choices may include (but are not limited to): SPAdes, BWA, Samtools, and QUAST.

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