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📌 Deprecation Notice

This repository is deprecated and will no longer be maintained by the Van Andel Institute Bioinformatics and Biostatistics Core. An updated fork with ongoing development and maintenance can be found here.

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This Snakemake workflow takes paired-end whole-genome bisulfite sequencing (WGBS) data and processes it using BISulfite-seq CUI Toolkit (BISCUIT).

BISCUIT was written to perform alignment, DNA methylation and mutation calling, and allele specific methylation from bisulfite sequencing data (https://huishenlab.github.io/biscuit/).

Download BISCUIT here: https://github.com/huishenlab/biscuit/releases/latest.

Components of the workflow

The following components are generally in order, but may run in a different order, depending on exact dependencies needed.

• [default off] Generate asset files used during QC related rules
• [default off] Modify and index genome reference to including methylation controls
• [default off] Trim adapters and/or hard clip R2
• [default off] Run Fastq Screen in bisulfite mode
• Run FastQC on raw FASTQ files
• Alignment, duplicate tagging, indexing, flagstat of input data (biscuitBlaster v1 and v2)
• Methylation information extraction (BED Format)
• Merge C and G beta values in CpG dinucleotide context
• [default off] SNP and Epiread extraction
• [default off] Run Preseq on aligned BAM
• MultiQC with BICUIT QC modules specifically for methyaltion data
• [default off] Generate plots of the observed / expected coverage ratio for different genomic features
• [default off] Generate percentage of covered CpGs and CpG island coverage figures
• [default off] QC methylated and unmethylated controls

Many options can be easily specified in the config.yaml! Otherwise, the commands in the Snakefile can also be modified to meet different needs.

Dependencies

The following dependencies are downloaded when running with --use-conda, otherwise you must have these in your PATH.

• snakemake (version 6.0+)
• biscuit (version 1.0.1+)
• htslib (version 1.12+)
• samtools (version 1.12+)
• samblaster
• parallel (preferably version 20201122)
• bedtools
• preseq (version 3.1.2+, must be compiled with htslib enabled)
• fastqc
• trim_galore
• fastq_screen (only required if running fastq_screen)
• bismark (only required if running fastq_screen)
• pigz
• python (version 3.7+)
  • pandas
  • numpy
  • matplotlib
• multiqc
• R (version 4.1.1+)
  • tidyverse (only required for plotting methylation controls)
  • ggplot2 (only required for plotting methylation controls)
  • patchwork (only required for plotting methylation controls)
  • viridislite (only required for plotting methylation controls)

Two things of note, 1) it is easiest when working with snakemake to install mamba using conda when running with --use-conda, and 2) it is preferable to install snakemake using conda, rather than using a module. This is due to potential conflicts between packages (such as matplotlib) that can be found in the snakemake module's python distrubtion and the conda installed python distribution.

Running the workflow

• Clone the repo (https://github.com/huishenlab/Biscuit_Snakemake_Workflow/tree/master).

  • git clone git@github.com:huishenlab/Biscuit_Snakemake_Workflow.git (SSH)
  • git clone https://github.com/huishenlab/Biscuit_Snakemake_Workflow.git (HTTPS)

• Place gzipped FASTQ files into raw_data/. Alternatively, you can specify the location of your gzipped FASTQ files in config/config.yaml.

• Replace the example config/samples.tsv with your own sample sheet containing:

  • A row for each sample
  • The following three columns for each row:
    • A. sample
    • B. fq1 (name of R1 file for sample in your raw data directory)
    • C. fq2 (name of R2 file for sample in your raw data directory)
    • D. Any other columns included are ignored Note, you can either edit config/samples.tsv in place or specify the path to your sample sheet in config/config.yaml. If you create your own sample sheet, make sure to include the header line as is seen in the example file.

• Modify the config.yaml to specify the appropriate

  • Reference genome
  • Biscuit index
  • Biscuit QC assets (https://github.com/huishenlab/biscuit/releases/latest)
  • Toggle optional workflow components
  • Set other run parameters in config/config.yaml
  • Turn on optional rules in config/config.yaml (change from False to True)
  • If you are using environmental modules on your system, you can set the locations in the corresponding location. By default, the pipeline will use conda/mamba to download the required packages. Note, if using the modules and a module is not available, snakemake gives a warning but will run successfully as long as the required executables are in the path.

• Then submit the rest workflow to an HPC using something similar to bin/run_snakemake_workflow.sh (e.g., qsub -q [queue_name] bin/run_snakemake_workflow.sh). bin/run_snakemake_workflow.sh works for a PBS/Torque queue system, but will need to be modifed to work with a Slurm or other system.

After the workflow

• The output files in config['output_directory']/analysis/pileup/ may be imported into a BSseq object using bicuiteer::readBiscuit().
• config['output_directory']/analysis/multiqc/multiqc_report.html contains the methylation-specific BISCUIT QC modules (https://huishenlab.github.io/biscuit/docs/alignment/QC.html)

Test dataset

This workflow comes with a working example dataset. To test the smakemake workflow on your system, place the 10 FASTQ files in bin/working_example_dataset into raw_data/ and use the default config/samples.tsv sample sheet. These example files can be mapped to the human genome.

Example default workflow - 1 sample

Helpful snakemake commands for debugging a workflow

For more information on Snakemake: https://snakemake.readthedocs.io/en/stable/

• Do a test run: snakemake -npr
• Unlock directory after a manually aborted run: snakemake --unlock --cores 1
• Create a workflow diagram for your run: snakemake --dag | dot -Tpng > my_dag.png
• Run pipeline from the command line: snakemake --use-conda --cores 1