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Hi-C based Genome Assembly


Hi-C is a method designed to capture chromosome configuration by combining probing proximity-based interactions and high-throughput sequencing. The intensity of these interactions is believed to be negatively correlated with physical distance on chromosomes. Therefore, Hi-C data is used to guide the clustering, ordering, and orienting of assembled sequences in a draft genome and anchoring those onto a certain number of chromosomes. This technology empowers a chromosome-level genome assembly in the absence of a population-based genetic map. Every single genome needs a Hi-C.

Service Details


Demo Results

Featured publications

Service Features

● Sequencing on Illumina NovaSeq with PE150.

● Service requires tissue samples, instead of extracted nucleic acids, to cross-link with formaldehyde and conserve the DNA-protein interactions.

● The Hi-C experiment involves restriction and end repair of the sticky ends with biotin, followed by circularization of the resulting blunt ends while preserving the interactions. The DNA is then pulled down with streptavidin beads and purified for subsequent library preparation.

Service Advantages


Overview of Hi-C
(Lieberman-Aiden E et al., Science, 2009)

● Eliminating the Need for Genetic Population Data: Hi-C substitutes the essential information required for contig anchoring.

● High marker density: leading to a high contig anchoring ratio at above 90%.

● Extensive Expertise and publication records: BMKGene has vast experience with >2000 cases of Hi-C Genome Assembly from 800 different species and various patents. Over 100 published cases with an accumulative impact factor of over 900.

● Highly skilled bioinformatics team:  with in-house patents and software copyrights for Hi-C experiments and data analysis, the self-developed visualization data software, enables manual block moving, reversing, revoking, and redoing.

● Post-Sales Support: Our commitment extends beyond project completion with a 3-month after-sale service period. During this time, we offer project follow-up, troubleshooting assistance, and Q&A sessions to address any queries related to the results.

● Comprehensive Annotation: we use multiple databases to functionally annotate the genes with identified variations and perform the corresponding enrichment analysis, providing insights on multiple research projects.

Service Specifications

Library preparation

Sequencing strategy

Recommended data output

Quality control

Hi-C library

Illumina NovaSeq PE150



Sample Requirements

Tissue or extracted nucleic acids

Required amount

Animal Viscera


Animal Muscle

Mammalian Blood


Poultry/Fish Blood

Plant- Fresh Leaf


Cultured Cells


Service Work Flow

Sample QC

Experiment design

sample delivery

Sample delivery

Pilot experiment

DNA extraction

Library Preparation

Library construction



Data analysis

Data analysis

After sale Services

After-sale services

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  • 流程图 羽莹-01

    1) Raw data QC

    2) Hi-C library QC: estimation of valid Hi-C interactions

    3) Hi-C assembly: clustering of contigs in groups, followed by contig ordering within each group and assigning contig orientation

    4) Hi-C evaluation

    Hi-C Library QC – estimation of Hi-C valid interaction pairs



    Hi-C Assembly – statistics


    Post-assembly evaluation – heatmap of signal intensity between bins


    Explore the advancements facilitated by BMKGene’s Hi-C assembly services through a curated collection of publications.

    Tian, T. et al. (2023) ‘Genome assembly and genetic dissection of a prominent drought-resistant maize germplasm’, Nature Genetics 2023 55:3, 55(3), pp. 496–506. doi: 10.1038/s41588-023-01297-y.

    Wang, Z. L. et al. (2020) ‘A Chromosome-Scale Assembly of the Asian Honeybee Apis cerana Genome’, Frontiers in Genetics, 11, p. 524140. doi: 10.3389/FGENE.2020.00279/BIBTEX.

    Zhang, F. et al. (2023) ‘Revealing evolution of tropane alkaloid biosynthesis by analyzing two genomes in the Solanaceae family’, Nature Communications 2023 14:1, 14(1), pp. 1–18. doi: 10.1038/s41467-023-37133-4.

    Zhang, X. et al. (2020) ‘Genomes of the Banyan Tree and Pollinator Wasp Provide Insights into Fig-Wasp Coevolution’, Cell, 183(4), pp. 875-889.e17. doi: 10.1016/J.CELL.2020.09.043

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