HiCUP
HiCUP (Hi-C User Pipeline) is a software tool to map quality filtering Hi-C raw data. The HiCUP algorithm includes functions for identification of Hi-C junctions, mapping read ends, pairing forward and reverse reads, and data filtering.
Topic
Epigenomics
Detail
Operation: Read mapping
Software interface: Command-line user interface
Language: Perl, R
License: GNU General Public License >=v3
Cost: Free
Version name: 0.8.0
Credit: The Medical Research Council and the Biotechnology and Biological Sciences Research Council of the UK.
Input: HIC raw sequence
Output: SAM, BAM
Contact: Steven Wingett steven.wingett@babraham.ac.uk
Collection: -
Maturity: Stable
Publications
- HiCUP: pipeline for mapping and processing Hi-C data.
- Wingett S, Ewels P, Furlan-Magaril M, Nagano T, Schoenfelder S, Fraser P, Andrews S. HiCUP: pipeline for mapping and processing Hi-C data. F1000Res. 2015 Nov 20;4:1310. doi: 10.12688/f1000research.7334.1. PMID: 26835000; PMCID: PMC4706059.
- https://doi.org/10.12688/f1000research.7334.1
- PMID: 26835000
- PMC: PMC4706059
Download and documentation
Source: https://www.bioinformatics.babraham.ac.uk/projects/download.html#hicup
Documentation: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html
Home page: http://www.bioinformatics.babraham.ac.uk/projects/hicup/
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