Bacterial Genome Assembly

This project uses Snakemake to assemble and annotate a bacterial genome from nanopore reads.

Description

This workflow uses the following tools to assemble and annotate a bacterial genome:

• Porechop(v0.2.4) for adapter trimming.
• Chopper(v0.9.0) for read filtering.
• Flye (v2.9.3) for genome assembly.
• raven (v1.8.3) for genome assembly.
• medaka (v1.11.3) for polishing the assemblies.
• seqkit (v2.7) to gets statistics of the assemblies.
• bakta (v1.9.2) for genome annotation.
• checkm2 (v1.0.1) to estimate the quality (completeness and contamination) of the genome.

At the end, there will be two different assemblies for your genome, one from flye and the other from raven in the assemblies folder. We chose the best assembly based on the checkm2 results, where we compare the genome qualities with this formula: perc_diff = (max(completeness)-min(completeness))*100/max(completeness). If the difference in completeness is less than 5%, we choose the assembly with the lowest number of contigs. If the difference is greater than 5%, we choose the assembly with the highest completeness.

Setup

1. Clone this repository to your local machine.
2. Navigate to the project directory.
3. Install miniconda from here.
4. Create a new conda environment to install the snakemake dependencies:

conda env create -n snakemake_env -c conda-forge snakemake mamba polars

5. Download the required databases:

• bakta
• checkm2

Configuration

Open the config/config.yaml file and modify the parameters according to your needs.

• work_dir: The location of this folder.
• results_dir : The directory where the results will be saved.
• env_dir : The directory where the conda files are found to create new environments.
• reads_dir : The location where the raw reads are stored in .fastq.gz.
• threads : The number of threads to use for the assembly and annotation steps.
• reads_size : The minimum size of the reads to be filtered.
• bakta_db : The location of the bakta database.
• checkm2_db : The location of the checkm2 database.

If using slurm, open the profile/config.yaml file and modify/add the following parameters if needed.

• qos
• partition
• account

Running the Workflow

To run the Snakemake workflow using slurm, execute the following command in your terminal:

conda activate snakemake_env
snakemake -s workflow/Snakefile --configfile config/config.yaml --conda-prefix snakemake_envs --use-conda --rerun-incomplete --profile profile/ 

Without slurm, you can run the workflow using the following command:

conda activate snakemake_env
snakemake -s workflow/Snakefile --configfile config/config.yaml --conda-prefix snakemake_envs --use-conda --rerun-incomplete