kellysthri/hicup-plus repository overview

⁠HiCUP+ (Hi-C User Pipeline Plus)

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HiCUP+ (HiCUP-plus) is a bioinformatics pipeline for processing Hi-C data.

HiCUP+⁠ is a fork of HiCUP⁠ with additional functionality. Please note that this is a maintained separately, a lthough efforts have been made to ensure compatibility with configurations with prior versions.

This version is maintained by H.U. Group Research Institute, G.K⁠ (Akiruno-shi, Tokyo, Japan). We acknowledge the original developers at Babraham Institute (Cambridge, English, United Kingdom

⁠Source Code

https://github.com/hugp-ri/hicup-plus/⁠

⁠Software installed

All software included has been release on open-source licenses.

⁠Dependencies

• Perl v5.30.0
• R v3.6.3 (tidyverse v1.3.2; plotly v4.10.1)
• samtools v1.10 (htslib v1.10-2-3)

⁠Supported aligners

• Bowtie v1.2.3
• Bowtie2 v2.3.5.1
• HiSAT2 v2.10

Note that the Dragen Bio-IT platform⁠ is not supported due to licensing restrictions and hardware requirements. The Dragen-OS/DRAGMAP⁠ v1.3.0-1 aligner is however included but may not be fully functional or give the same results as the preprint. It is for demonstration purposes only.

⁠Documentation

https://hicup-plus.readthedocs.io/⁠

⁠How to cite HiCUP+

Please cite the following preprint:

Kelly, S. T. & Yuhara, S. (2022) HiCUP-Plus: a fast open-source pipeline for accurately processing large scale Hi-C sequence data. bioRxiv 2022.05.18.492393; doi: 10.1101/2022.05.18.492393⁠