Introduction

Hi-C User Pipeline (HiCUP) is a bioinformatics pipeline for processing Hi-C data. The pipeline takes and maps FASTQ data against a reference genome and filters out frequently encountered experimental artefacts. The pipeline produces paired-read files in SAM/BAM format, each read pair corresponding to a putative Hi-C di-tag. HiCUP also produces summary statistics at each stage of the pipeline providing quality control, helping pinpoint potential problems and refine the experimental protocol. HiCUP comprises five Perl scripts (in addition to the control script) for analysing Hi-C sequence data.

For more information, visit the HiCUP official website.

Programming language: Perl

Brief description: a bioinformatics pipeline for processing Hi-C data.

Open source license: LGPL-3.0