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Background:In eukaryotic genome,chromatin is not randomly distributed in cell nuclei,but instead is organized into higher-order structures.Emerging evidence indicates that these higher-order chromatin structures play important roles in regulating genome functions such as transcription and DNA replication.With the advancement in 3C (chromosome conformation capture) based technologies,Hi-C has been widely used to investigate genome-wide longrange chromatin interactions during cellular differentiation and oncogenesis.Since the first publication of Hi-C assay in 2009,lots of bioinformatic tools have been implemented for processing Hi-C data from mapping raw reads to normalizing contact matrix and high interpretation,either providing a whole workflow pipeline or focusing on a particular process.Results:This article reviews the general Hi-C data processing workflow and the currently popular Hi-C data processing tools.We highlight on how these tools are used for a full interpretation of Hi-C results.Conclusions:Hi-C assay is a powerful tool to investigate the higher-order chromatin structure.Continued development of novel methods for Hi-C data analysis will be necessary for better understanding the regulatory function of genome organization.