nfcore/methylseq repository overview

⁠Introduction

nf-core/methylseq is a bioinformatics analysis pipeline used for Methylation (Bisulfite) sequencing data. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.

The pipeline is built using Nextflow⁠, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

⁠Pipeline Summary

The pipeline allows you to choose between running either Bismark⁠ or bwa-meth⁠ / MethylDackel⁠. Choose between workflows by using --aligner bismark (default, uses bowtie2 for alignment), --aligner bismark_hisat or --aligner bwameth.

⁠Quick Start

1. Install nextflow⁠ (>=20.04.0)

2. Install any of Docker⁠, Singularity⁠, Podman⁠, Shifter⁠ or Charliecloud⁠ for full pipeline reproducibility (please only use Conda⁠ as a last resort; see docs⁠)

3. Download the pipeline and test it on a minimal dataset with a single command:

   nextflow run nf-core/methylseq -profile test,<docker/singularity/podman/shifter/charliecloud/conda/institute>
   

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   Please check nf-core/configs⁠ to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile <institute> in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment.

4. Start running your own analysis!

   nextflow run nf-core/methylseq -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input '*_R{1,2}.fastq.gz' --genome GRCh37
   

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See usage docs⁠ for all of the available options when running the pipeline.

⁠Documentation

The nf-core/methylseq pipeline comes with documentation about the pipeline: usage⁠ and output⁠.

⁠Credits

These scripts were originally written for use at the National Genomics Infrastructure⁠ at SciLifeLab⁠ in Stockholm, Sweden.

• Main author:
  • Phil Ewels (@ewels⁠)
• Contributors:
  • Rickard Hammarén (@Hammarn⁠)
  • Alexander Peltzer (@apeltzer⁠)
  • Patrick Hüther (@phue⁠)

⁠Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines⁠.

For further information or help, don't hesitate to get in touch on the Slack #methylseq channel⁠ (you can join with this invite⁠).

⁠Citations

If you use nf-core/methylseq for your analysis, please cite it using the following doi: 10.5281/zenodo.2555454⁠

You can cite the nf-core publication as follows:

In addition, references of tools and data used in this pipeline are as follows:

• FastQC - https://www.bioinformatics.babraham.ac.uk/projects/fastqc/⁠
• Trim Galore! - https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/⁠
• Bismark - 10.1093/bioinformatics/btr167⁠
• bwa-meth - arXiv:1401.1129⁠
• Picard - http://broadinstitute.github.io/picard/⁠
• Qualimap - 10.1093/bioinformatics/btv566⁠
• Preseq - 10.1038/nmeth.2375⁠
• MultiQC - 10.1093/bioinformatics/btw354⁠