---
title: "HiCUP: pipeline for mapping and processing Hi-C data"
url: "https://phil.ewels.co.uk/publications/2015/wingett-f1000research"
site: "phil.ewels.co.uk"
author: "Phil Ewels"
section: "Publications"
journal: "F1000Research"
published: "2015-11-20"
doi: "https://doi.org/10.12688/f1000research.7334.1"
authors: "Steven W. Wingett, Philip Ewels, Mayra Furlan-Magaril, Takashi Nagano, Stefan Schoenfelder, Peter Fraser, Simon Andrews"
---

# HiCUP: pipeline for mapping and processing Hi-C data

HiCUP is a pipeline for processing sequence data generated by Hi-C and Capture Hi-C (CHi-C) experiments, which are techniques used to investigate three-dimensional genomic organisation. The pipeline maps data to a specified reference genome and removes artefacts that would otherwise hinder subsequent analysis. HiCUP also produces an easy-to-interpret yet detailed quality control (QC) report that assists in refining experimental protocols for future studies. The software is freely available and has already been used for processing Hi-C and CHi-C data in several recently published peer-reviewed studies.

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From the personal website of Phil Ewels, a software developer and bioinformatician in Stockholm, Sweden: https://phil.ewels.co.uk/
The whole site as Markdown: https://phil.ewels.co.uk/llms.txt