Hi-C-based Genome Assembly

Chromosome-level genome construction by Hi-C

Hi-C is required for every genome construction

Service Overview


Hi-C is a novel technology combining chromosome conformation capture and high-throughput sequencing. DNA fragments of long linear distance while close in spatial structures are fixed and enriched for Pair-end sequencing. This technology empowers us to reveal the interactions between chromosome compartments and 3D structure of genome, which provides vital clues for novel intergenetic regulatory mechanisms.

Schematic representation of hierarchical chromatin organization (Ezgi Süheyla et al., Nature Plants 2018)

There is no need of genetic map for genome assembly to chromosome-level. Every single genome needs a Hi-C.

Hi-C Advantages

  • More than 90% reads are alignable on chromosomes
  • No need to construct a genetic population
  • More efficient and cost-effective compared to genetic mapping based assembly
  • Intelligent algorithm for automatic contig clustering and ordering 

Principles of Hi-C

In situ Hi-C library construction procedures are applied as shown in the figure, including DNA crosslinking, digestion with restricted enzyme, end filling, ligating, DNA purification and pulling down, Paired-end sequencing.

Applications of Hi-C

Hi-C based structural variation analysis on Gossypium hirsutum(Yang Z et al.,Nature Communications 2019)

Hi-C based genome assembly of gossypium hirsutumm and Gossypium barbadense(Wang et al.,Nature Genetics 2018)


Hi-C based TAD analysis (Wang et al.,Nature Genetics 2018)

Advantages of Hi-C Based Genome Assembly

1. Positioning on chromosome can be achieved with single material. There is no need of constructing genetic population.
Genetic population is not always available, especially in terms of most higher animals, wild animals and plants, fruit trees, etc. Hi-C positioning is based on different interaction frequencies between DNA with different linear distance, Therefore, no genetic population is needed.

2. Higher density of markers leading to more anchored contigs on chromosomes.
Compared to genetic mapping, chromosome interactions are markers with much higher density. The markers of high density allows anchoring of much shorter scaffold. Generally, more than 90% of genome sequences can be anchored on chromosomes by Hi-C.

3. Assembled genome can be corrected.
Genome correction is available basing on the interaction frequency between scaffold.

Bioinformatic Analysis

1. Raw data quality control
2. Hi-C library quality control
3. Hi-C genome assembly

  • Clustering contigs or scaffolds to chromosome groups
  • Ordering contigs or scaffolds within group
  • assigning relative orientations to individual contig or scaffold
4. Post-assembly evaluation
  • Evaluation based on reference genome of affinis species
  • Evaluation based on genetic markers.

Hi-C with Biomarker Technologies

Massive experience in Hi-C technology, achieving assembly of approx. 300 species and construction of approx. 1,000 Hi-C library.

Customized Restrict Enzyme design based on species, achieving over 93% valid interaction pairs in Hi-C library and average ratio of 68%.

Assembly of polyploid species was achieved by Hi-C here, with up to 100% anchoring of genome onto chromosomes.

We owns several experimental patents and bioinformatic software copyrights empowering us to provide the best Hi-C service.

Visual bioinformatic analysis system with various tools for plotting figures of your preference.

Project Workflow

Sample delivery
Library construction and sequencing
Data analysis
Final report
After-sale technical support

Work with Biomarker Technologies

50+ skilled experts in analysis
60+ successful cases
Highly-experienced technical team
3 distributed computer cluster servers
30X+ sequencing depth
Optimized reports delivery
Professional after-sale support
Rapid analysis


1What is Hi-C?
Hi-C is a combined technology of Chromosome conformation capture and high-throughput sequencing. It captures interacted DNA fragments through whole genome based on their physical spatial distance. These captured DNA interactions could be sequenced and analyzed to achieve chromosome-level genome assembly and reveal chromosome 3D-structure. Moreover, combining with ChIP-Seq and transcriptome data, gene regulatory network can be built to identify novel molecular mechanism of phenotypes.
2How does Hi-C help in genome assembly?
1. The most important achievement of Hi-C is to anchor sequence pieces (contigs or scaffolds) onto chromosomes. (Similar to genetic map) 2, Hi-C data can be used for genome correction. 3. Contig N50 can be increased.
3What's the difference between Hi-C and genetic map?
1. By Hi-C, chromosome construction can be done with individuals 2. The assignment ratio of sequences to chromosomes can be as high as over 90% by Hi-C 3. QTL-mapping can not be achieved by Hi-C
4What's the requirements of samples for Hi-C analysis?
1. Plants: Live seedling. 2. Animal: whole blood 3. Contact us for more detailed requirements on other sample types.