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.
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.
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.
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.
The primary outputs of the workflow include:
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