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Arima-HiC Genome Assembly: A critical component of VGP Phase 1

Arima Genomics is a technology partner of the VGP Phase 1. Long-read PacBio sequencing is performed to generate the initial contigs, followed by long-range scaffolding approaches to assemble contigs into chromosomes. Image courtesy of Vertebrate Genomes Project


Reference-Quality, Chromosome-Spanning Assemblies

Using long-range information to transform contigs into chromosomes


The Arima-HiC kit is a highly simplified and robust protocol that streamlines Hi-C to a 6-hour workflow, followed by library prep and next-generation sequencing. The Arima-HiC kit empowers researchers to leverage Hi-C technology to detect and correct misjoin errors in draft assemblies, assign contigs to chromosomes de novo, and order and orient contigs into chromosome-scale scaffolds.

  • Proven performance—higher long-range signals lead to the most accurate and contiguous chromosome-spanning assemblies.
  • Fast and user-friendly workflow—expedite time-to-insight with a rapid, 6-hour, Hi-C workflow.
  • Assured quality—ascertain library quality before sequencing with quick and easy library QC steps.
  • Efficient data collection—obtain multiple data types from a single assay, such as long-range sequence information and genome structure.
  • No need for high molecular weight (HMW) DNA extraction—enable the analysis of a wide variety of sample types and qualities.

Hi-C for De Novo Genome Assembly Studies

Generating a high-quality genome assembly is a critical starting point towards understanding the biology of an organism. Assembly approaches are shifting from the lower contiguity methods using solely Illumina shotgun sequencing to approaches incorporating long-range sequence information to enable a more contiguous and comprehensive genome assembly. Multiple methods generate long-range sequence information, such as direct sequencing of longer DNA molecules using long reads, optical mapping of long DNA molecules, or biochemical sample preparations innovations followed by short-read sequencing.

Within the three-dimensional (3D) space of a cell, chromosomes are highly folded structures whereby DNA segments that are spatially proximal in 3D space can be far apart along the linear chromosome. Hi-C is a proximity ligation sample preparation method that detects spatially proximal DNA interactions within cells; in doing so, it leverages chromosome folding properties to preserve long-range sequence information that is then sequenced using Illumina sequencing. This “map” of DNA interactions uniquely captures a biological property of chromosomes within cells, and therefore can be used to assign contigs to chromosomes de novo and determine the order and orientation of contigs along the chromosome, collectively producing chromosome-scale scaffolds.

By capturing the sequence and structure of chromosomes within cells to enable chromosome-scale scaffolding, Hi-C has emerged as a powerful tool for deriving high-quality and contiguous genome assemblies and is widely used today in a variety of research areas across the plant and animal kingdoms, including large-scale genome assembly consortia projects such as the Vertebrate Genome Project (VGP).


Comprehensive Arima-HiC Workflow


Rapid 6-hour protocol

  • Chromatin cross-linking
  • Digest crosslinked chromatin
  • Ligation
  • QC Check

Pre-validated library prep protocols

  • KAPA HyperPrep
  • Swift Accel-NGS 2S Plus
  • Agilent SureSelect XT
  • Illumina TruSeq
  • NEBNext Ultra II
  • Other

Optimized for
next-generation sequencers

  • Illumina NovaSeq
  • Illumina HiSeq
  • Illumina NextSeq
  • Illumina MiSeq
  • BGI-Seq

Powerful analysis with open source tools

  • Arima Genomics Mapping Pipeline
  • Other



The Arima-HiC Kit and Service for Chromosome-Spanning Assemblies

App Note:

The Role of Hi-C in Genome Assembly