Introduction

nf-core/brimeth is a bioinformatics pipeline that take a bam file from ONT sequencing, containing modbase information in MM,ML tags, writes fastq file, performs QC and filtering, maps to reference genome, and write a bedmethyl file.

1. Convert bam to fastq (samtools bam2fq), carrying the MM,ML tags for modified base
2. Perform quality control (FastQC) and reads quality and length filtering (Chopper)
3. Map fastq to reference genome (minimap2)
4. Perform quality control (Qualimap, Samtools stats
5. Extract methylation calls per site into a bedmethyl file (modkit)
6. Present QC for raw reads (MultiQC)

Usage

Note If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

sample,bam
sample1,file.bam

Each row represents a bam file

Now, you can run the pipeline using:

nextflow run nf-core/brimeth \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --fasta reference genome \
   --outdir <OUTDIR>

Warning: Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

For more details, please refer to the usage documentation and the parameter documentation.

Pipeline output

To see the the results of a test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

Credits

nf-core/brimeth was originally written by Yusmiati Liau and Christopher Hakkaart

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 #brimeth channel (you can join with this invite).

Citations

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.