Workflow Pore-C

This repository contains a nextflow workflow to convert data generated with the Pore-C protocol to outputs in a variety of standard file formats used by downstream tools.

Introduction

Pore-C is an end-to-end workflow unique to Oxford Nanopore which combines chromatin conformation capture (3C) with direct, long nanopore sequencing reads. With nanopore reads, long-range, multi-way contact information can be obtained. Pore-C can be used to scaffold and improve the quality of existing genome assemblies to generate chromosome-scale assemblies, discover unique insights into the higher-order genome organisation of a species of interest, and reveal epigenetic information for a more comprehensive understanding of gene regulation. Find out more about the workflow here

This nextflow workflow will create virtual digests of the genome using the pore-c-py package, align the resulting monomers against a reference genome with minimap2 and then filter spurious alignments, detect ligation junctions and assign fragments. The resulting BAM alignment file can be used with downstream tools.

Optionally the workflow can output a pairs format report which uses pairtools.

Quickstart

The workflow uses nextflow to manage compute and software resources, as such nextflow will need to be installed before attempting to run the workflow.

The workflow can currently be run using either Docker or Singularity to provide isolation of the required software. Both methods are automated out-of-the-box provided either docker or Singularity is installed.

It is not required to clone or download the git repository in order to run the workflow. For more information on running EPI2ME Labs workflows visit our website.

Workflow options

To obtain the workflow, having installed nextflow, users can run:

nextflow run epi2me-labs/wf-pore-c --help

to see the options for the workflow.

Workflow outputs

The primary outputs of the workflow include:

• Coordinate sorted Bam and index
• Name sorted Bam

Optional outputs

• 4DN-format pairs file

Useful links

• nextflow
• docker
• pore-c-py
• minimap2
• pairtools
• Pore-C: multi-contact, chromosome conformation capture for both genome-wide and targeted analyses.
• Visit the Nanopore Community for guidance through every step of the Pore-C workflow. Optimised Nanopore workflows have been developed: blood samples, plants, and cell culture, animal, or insect tissues – the method is simple and scalable.

References

Deshpande, A.S., Ulahannan, N., Pendleton, M. et al. Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing. Nat Biotechnol (2022). https://doi.org/10.1038/s41587-022-01289-z: https://www.nature.com/articles/s41587-022-01289-z