Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
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 uses Docker / Singularity containers making installation trivial and results highly reproducible.
On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the nf-core website.
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
|Generate Reference Genome Index (optional)
|Raw data QC
|Adapter sequence trimming
|Extract methylation calls
Install any of
Singularity(you can follow this tutorial),
Charliecloudfor full pipeline reproducibility (you can use
Condaboth to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see docs).
Download the pipeline and test it on a minimal dataset with a single command:
- 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
singularityand set the appropriate execution settings for your local compute environment.
- If you are using
singularitythen the pipeline will auto-detect this and attempt to download the Singularity images directly as opposed to performing a conversion from Docker images. If you are persistently observing issues downloading Singularity images directly due to timeout or network issues then please use the
--singularity_pull_docker_containerparameter to pull and convert the Docker image instead. It is also highly recommended to use the
singularity.cacheDirsettings to store the images in a central location for future pipeline runs.
- If you are using
conda, it is highly recommended to use the
conda.cacheDirsettings to store the environments in a central location for future pipeline runs.
Start running your own analysis!
- Main author:
- Phil Ewels (@ewels)
Contributions and Support
If you would like to contribute to this pipeline, please see the contributing guidelines.
If you use nf-core/methylseq for your analysis, please cite it using the following doi: 10.5281/zenodo.1343417
An extensive list of references for the tools used by the pipeline can be found in the
You can cite the
nf-core publication as follows:
The nf-core framework for community-curated bioinformatics pipelines.
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.