author Jani
Schematic of the gs-meth pipeline. In yellow the pre-existing nf-core pipeline, and the blue shows the extensions that have been added to the pipeline.
The GENE-SWitCH project has received funding from the European Union’s Horizon 2020 ( https://ec.europ a.eu/programmes/horizon2020/ ) research and innovation program under Grant Agreement No 817998. This repository reflects only the listed contributors views. Neither the European Commission nor its Agency REA are responsible for any use that may be made of the information it contains.
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.
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 |
-
Install
nextflow
-
Install any of
Docker
,Singularity
,Podman
,Shifter
orCharliecloud
for full pipeline reproducibility (please only useConda
as a last resort; see docs) -
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>
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. -
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
See usage docs for all of the available options when running the pipeline.
The nf-core/methylseq pipeline comes with documentation about the pipeline: usage and output.
These scripts were originally written for use at the National Genomics Infrastructure at SciLifeLab in Stockholm, Sweden.
- Main author:
- Phil Ewels (@ewels)
- Contributors:
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).
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:
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.
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