A snakemake workflow for basic whole-genome bisulfite sequencing (WGBS) data analysis

Requirements

Before start running the workflow, please ensure that the following software is installed in your environment:

• Snakemake (>=8.14.0)
• SOAPnuke (>=2.0)
• Bismark (>=0.24.2)

Installation

git clone https://github.com/axxxxx08/WGBS.git

Usages

1. Reference genome preparation

A reference genome is required for the Bismark alignment step. The reference genome file should be placed in a directory and must be in FastA format (.fa or .fasta).

bismark_genome_preparation --bowtie2/--hisat2 <path_to_genome_folder>

Tips: You can choose either bowtie2 or hisat2 as your aligner, but it must be consistent with the alignment step (default: bowtie2).

2. Generate your own config file

To generate a config file for running Snakemake, you can run the script generate_config.py in the workflow/scripts directory. Or, write your own config file and place it in the workflow/config directory.

generate_config.py --samplefile sample.txt --outdir your_output_dir --config_output workflow/config --ref_dir your_reference_genome_dir

Tips: The sample file should be formatted like below:

id	fq1	fq2
Sample1	/dir/sample1_1.fq.gz	/dir/sample1_2.fq.gz
Sample2	/dir/sample2_1.fq.gz	/dir/sample2_2.fq.gz

3. Running snakemake

Now you can use Snakemake to run your samples. Before running, you can add --dryrun to Snakemake to check for any potential problems.

snakemake -s workflow/Snakefile -c cores --dryrun

If there are no problems:

snakemake -s workflow/Snakefile -c cores

Notes:

• Check the number of CPUs on your server, and choose appropriate cores and threads when running Snakemake. The threads can be manually adjusted in the config file.
• Choose proper parameters for each step; these can be manually changed in the .smk files within the workflow/rules directory.
• Verify the config file to ensure the correct paths of output directory, sample file, and reference genome are specified.