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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 could 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 absence of population-based genetic map. Every single genome needs a Hi-C.

Platform:Illumina NovaSeq Platform / DNBSEQ

Service Details

Demo Results

Case Study

Service Advantages


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

● No need in constructing genetic population for contig anchoring;
● Higher marker density leading to higher contigs anchoring ratio at above 90%;
● Enables evaluation and corrections on existing genome assemblies;
● Shorter turn-around time with higher accuracy in genome assembly;
● Abundant experience with over 1000 Hi-C libraries constructed for over 500 species;
● Over 100 successful cases with accumulative published impact factor of over 760;
● Hi-C based genome assembly for polyploid genome, 100% anchoring rate was achieved in previous project;
● In-house patents and software copyrights for Hi-C experiments and data analysis;
● Self-developed visualized data tuning software, enables manual block moving, reversing, revoking and redoing.

Service Specifications


Library Type




Read Length
Recommend Strategy
Illumina NovaSeq
≥ 100X

Bioinformatics analyses

● Raw data quality control

● Hi-C library quality control

● Hi-C based genome assembly

● Post-assembly evaluation

HiC workflow

Sample Requirements and Delivery

Sample Requirements:



Frozen tissue:  1-2g per library
Cells:  1x 10^7 cells per library
Frozen tissue: 1g per library
Frozen tissue: 1-2g per library


*We strongly recommend sending at least 2 aliquots (1 g each) for the Hi-C experiment.

Recommended Sample Delivery

Container: 2 ml centrifuge tube (Tin foil is not recommended)
For most of samples, we recommend not to preserve in ethanol.
Sample labeling: Samples need to be clearly labeled and identical to submitted sample information form.
Shipment: Dry-ice: Samples need to be packed in bags first and buried in dry-ice.

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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  • *Demo results shown here are all from genomes published with Biomarker Technologies

    1.Hi-C interaction heat map of Camptotheca acuminata genome. As shown on the map, the intensity of interactions is negatively correlated with the linear distance, which indicates a highly-accurate chromosome-level assembly. (Anchoring ratio: 96.03%)


    Kang M et al., Nature Communications, 2021


    2.Hi-C facilitated the validation of inversions between Gossypium hirsutum L. TM-1 A06 and G. arboreum Chr06


    Yang Z et al., Nature Communications, 2019



    3.Assembly and biallelic differentiation of the cassava genome SC205. Hi-C heatmap shown clear split in homologous chromosomes. 


    Hu W et al., Molecular Plant, 2021



    4.Hi-C heatmap on two Ficus species genome assembly: F.microcarpa (anchoring ratio: 99.3%) and F.hispida (anchoring ratio: 99.7%) 

    Zhang X et al., Cell, 2020



    BMK Case

    Genomes Of The Banyan Tree And Pollinator Wasp Provide Insights Into Fig-wasp Coevolution 

    Published: Cell, 2020

    Sequencing strategy:

    F. microcarpa genome: Approx. 84 X PacBio RSII (36.87 Gb) + Hi-C (44 Gb)

    F. hispida genome: Approx. 97 X PacBio RSII (36.12 Gb) + Hi-C (60 Gb)

    Eupristina verticillata genome: Approx. 170 X PacBio RSII (65 Gb)

    Key results

    1.Two banyan tree genomes and one pollinator wasp genome were constructed using PacBio sequencing, Hi-C and linkage map.
    (1)F. microcarpa genome: An assembly of 426 Mb (97.7% of estimated genome size) was established with contig N50 of 908 Kb, BUSCO score of 95.6%. In total of 423 Mb sequences were anchored to 13 chromosomes by Hi-C. Genome annotation yielded 29,416 protein-coding genes.
    (2)F. Hispida genome: An assembly of 360 Mb (97.3% of estimated genome size) was yield with contig N50 of 492 Kb and BUSCO score of 97.4%. A total of 359 Mb sequences were anchored on 14 chromosomes by Hi-C and highly identical to high-density linkage map.
    (3)Eupristina verticillata genome: An assembly of 387 Mb (Estimated genome size: 382 Mb) was established with contig N50 of 3.1 Mb and BUSCO score of 97.7%.

    2.Comparative genomics analysis revealed great number of structure variations between two Ficus genomes, which provided invaluable genetic resource for adaptive evolution studies. This study, for the first time, provided insights into Fig-wasp coevolution at genomic-level.


    Circos diagram on genomic features of two Ficus genomes, including chromosomes, segmental duplications (SDs), transposons(LTR, TEs, DNA TEs), gene expression and synteny


    Identification of the Y chromosome and sex determination candidate gene


    Zhang, X. , et al. “Genomes of the Banyan Tree and Pollinator Wasp Provide Insights into Fig-Wasp Coevolution.” Cell 183.4(2020).

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