Pore-C Tools¶

A command-line toolkit to work with Pore-C data

This package is designed to analyse the data from multi-contact pore-C reads. It is similar to the pairtools package in scope, however it is specifically designed to handle multi-contact reads (aka c-walks). It carries out the following operations:

pre-processing a reference genome to generate auxiliary files used in downstream analyses
creating virtual digests of the reference genome
processing BAM files to filter spurious alignments, detect ligation junctions and assign fragments
converting the resulting contacts to a pairs format and a COO-formatted matrix compatible with Cooler for downstream processing.

The recommended way to run Pore-C tools is through the associated Pore-C-Snakemake pipeline. It wraps the pore-C commands and also handles some of the analysis steps outside the scope of pore-C tools such as read alignment and conversion of output files to .cool format. If you want to run the tools outside of this pipeline please see the section below on