nf-core/methylseq
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
2.0.0
). The latest
stable release is
2.6.0
.
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 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.
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
.
Step | Bismark workflow | bwa-meth workflow |
---|---|---|
Generate Reference Genome Index (optional) | Bismark | bwa-meth |
Raw data QC | FastQC | FastQC |
Adapter sequence trimming | Trim Galore! | Trim Galore! |
Align Reads | Bismark | bwa-meth |
Deduplicate Alignments | Bismark | Picard MarkDuplicates |
Extract methylation calls | Bismark | MethylDackel |
Sample report | Bismark | - |
Summary Report | Bismark | - |
Alignment QC | Qualimap | Qualimap |
Sample complexity | Preseq | Preseq |
Project Report | MultiQC | MultiQC |
Quick Start
-
Install
Nextflow
(>=21.10.3
) -
Install any of
Docker
,Singularity
(you can follow this tutorial),Podman
,Shifter
orCharliecloud
for full pipeline reproducibility (you can useConda
both 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 eitherdocker
orsingularity
and set the appropriate execution settings for your local compute environment. - If you are using
singularity
then 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_container
parameter to pull and convert the Docker image instead. It is also highly recommended to use theNXF_SINGULARITY_CACHEDIR
orsingularity.cacheDir
settings to store the images in a central location for future pipeline runs. - If you are using
conda
, it is highly recommended to use theNXF_CONDA_CACHEDIR
orconda.cacheDir
settings to store the environments in a central location for future pipeline runs.
-
Start running your own analysis!
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:
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.1343417
An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md
file.
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.