pycoMethFlow

pycoMethFlow is a Nextflow pipeline for running minimap2 + nanopolish call-methylation + pycoMeth on multiple samples and across multiple infrastructures in a streamlined, portable and reproducible manner.

Getting started

Prerequisites

Nextflow
Docker or Singularity

Installation

git clone https://github.com/MaestSi/pycoMethFlow.git
cd pycoMethFlow
chmod 755 *

Usage

The pycoMethFlow pipeline requires you to open pycomethflow.conf configuration file and set the desired options. Then, you can run the pipeline using either docker or singularity environments just specifying a value for the -profile variable.

nextflow -c pycomethflow.conf run pycomethflow.nf \
--samples = "samples.txt" \
--results_dir = "results_dir" \
--reference = "file.fasta" \
--gff = "file.gff" \
-profile docker

    Mandatory argument:
    -profile                        Configuration profile to use. Available: docker, singularity
    Other mandatory arguments which may be specified in the pycomethflow.conf file
      --samples                     Path to tab separated sample sheet containing sample_name /path/to/file.fastq /path/to/fast5_dir /path/to/sequencing_summary.txt
      --results_dir                 Directory where results are stored
      --reference                   Reference file in fasta format
      --gff                         Annotation file in gff3 format

Citation

For further information, please refer to the following manuscripts:

Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018 Sep 15;34(18):3094-3100. doi: 10.1093/bioinformatics/bty191. PMID: 29750242; PMCID: PMC6137996.

Simpson, J., Workman, R., Zuzarte, P. et al. Detecting DNA cytosine methylation using nanopore sequencing. Nat Methods 14, 407–410 (2017). https://doi.org/10.1038/nmeth.4184

PycoMeth: A toolbox for differential methylation testing from Nanopore methylation calls. Rene Snajder, Oliver Stegle, Marc Jan Bonder. bioRxiv 2022.02.16.480699; doi: https://doi.org/10.1101/2022.02.16.480699