mydennislab/CiFi: CiFi: Accurate long-read chromosome conformation capture with low-input requirements

Pipeline for mapping of CiFi data as well as conversion into contact matrix .hic file. This also includes all downstream analysis including:

• coverage comparisons
• segment mapping visualization
• segment summary statistics
• intrachromosomal distance between pairs
• MAPQ comparisons across different genomic bins
• contact signal correlation
• TAD calling and concordance