Monkeypox Metagenomics Analysis with ONT Reads

This repo contains analysis workflow for Oxford Nanopore reads.

You can use this program to generate monkeypox whole genome from your "*.fastq" files obtained as a result of metagenomic analysis.

Download and install anaconda

Add channels

conda config --add channels conda-forge\
conda config --add channels bioconda\
conda config --add channels daler\
conda config --add channels defaults\

Download the Analysis pipeline

git clone https://github.com/cinnetcrash/Lymra-Ont.git

Change directory to the dowloaded folder

cd Lymra-Ont

Create conda environment. All the packages are listed in the environment.yaml file

conda env create -f environment.yaml

Activate the analysis environment

conda activate Lymra-Ont

Add permission to all scripts

chmod +x *.{py,sh}

Install python packages using pip

pip install -r pip-requirements.txt

To use snakemake instead of conda first install snakemake environment

mamba create -c conda-forge -c bioconda -n snakemake snakemake
conda activate snakemake

Copy your read files to the data/ folder then execute the snakemake command

snakemake -s Snakefile --use-conda --cores 12

Use this citation to cite my efforts

Gültekin Ünal, 2022. Lymra Oxford Nanopore Monkeypox Anaylsis Tool https://github.com/cinnetcrash/Lymra-Ont