Background It is becoming increasingly important to understand the mechanism of regulatory elements on target genes in long-range genomic distance. 3C (Chromosome Conformation Capture) and its derived methods are now widely applied to investigate genome organizations and gene regulation. Digestion-Ligation-Only Hi-C (DLO Hi-C) is a new technology with high efficiency and effective cost for whole-genome chromosome conformation capture.Results Here, we introduce DLO Hi-C Tool, a flexible and versatile pipeline for processing DLO Hi-C data from raw sequencing reads to normalized contact maps and providing quality controls for different steps. It includes more efficient iterative mapping and linker filtering. We applied DLO Hi-C Tool to different DLO Hi-C datasets, and demonstrated its ability of processing large data in multi-threading.Conclusions DLO Hi-C Tool is suitable for processing DLO Hi-C and in situ DLO Hi-C datasets. It is convenient and efficient for DLO Hi-C data processing.*   ### Abbreviations        3C    :   C hromosome C onformation C apture    3D    :   Three-Dimensional    BWA    :   Burrows-Wheeler Alignment    ChIA-PET    :   Chromatin Interaction Analysis by Paired-End Tag Sequencing    DLO Hi-C    :   Digestion-Ligation-Only Hi-C    HTML    :   HyperText Markup Language    PAGE    :   PolyacrylAmide Gel Electrophoresis    PCR    :   Polymerase Chain Reaction    SNP    :   Single Nucleotide Polymorphism    TADs    :   Topologically Associating Domains

DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis