/nanopore_cfdna

Primary LanguageGroovy

Deconvolution Workflow

This repository contains a nextflow workflow for deconvoluting a complex mixture of DNA into mixture proportions using nanopore methylation calls. A task useful for cell-free DNA analysis. Input files can either start from raw .fast5 files or basecalled .bam files. Deconvolution Pipeline

Set up

The following programs should be installed into your environment

  1. guppy
  2. nanomix
  3. mbtools

Quickstart

Make a new directory for your run. Inside that directory make another directory called data:

mkdir dev1
cd dev1
mkdir data

Then inside the data directory make symbolic links to the directories where the nanopore runs are kept.

cd data
ln -s <PATH_TO_DATA>

Then whilst in the run directory execute the nextflow script with the following command which takes as input the path to this repository.

cd ..
nextflow run <.../nanopore_cfdna/>

To view parameters for deconvolution run

nextflow run <.../nanopore_cfdna/> --help

Results

  • bams directory contains modified bam files
  • methylomes directory contains the methylome files (counts of modification calls)
  • mixture_proportions contains sigma vectors for each sample
  • plots contains a visualization of the results