DNA Methylation analysis of APPNLGF mouse brains

This is a snakemake pipeline that takes Oxford Nanopore Sequencing (ONT) data (fastq) as input, generates fastq stats using nanostat, map the reads to the genome using minimap2 and uses sniffles for calling structural variants.

Getting Started

Input

• ONT fastq reads
• Reference genome assembly in fasta format

Depedencies

• miniconda
• The rest of the dependencies (including snakemake) are installed via conda through the environment.yml file

Clone the directory:

git clone --recursive https://github.com/umranyaman/ONT_DNA_pipeline.git

Create conda environment for the pipeline which will install all the dependencies:

cd ONT_DNA_pipeline
conda env create -f environment.yml

Usage

Edit config.yml to set up the working directory and input files/directories. snakemake command should be issued from within the pipeline directory. Please note that before you run any of the snakemake commands, make sure to first activate the conda environment using the command conda activate ONT_DNA_pipeline.

cd ONT_DNA_pipeline
conda activate ONT_DNA_pipeline
snakemake --use-conda -j <num_cores> all

It is a good idea to do a dry run (using -n parameter) to view what would be done by the pipeline before executing the pipeline.

snakemake --use-conda -n all

Output

working directory  
|--- config.yml           # a copy of the parameters used in the pipeline  
|--- Nanostat/  
     |-- # output of nanostat - fastq stats   
|--- Mapping/  
     |-- # output of minimap2 - aligned reads  
|--- sniffles/  
     |-- # output of sniffles - vcf with SVs