Plant/Animal Genome Assembly

Chicago, Dovetail Hi-C and HiRise for chromosome level genome assembly

If your organism doesn't have a reference genome, or your draft assembly needs improvement, we can make it happen—in just weeks.

From agriculture and ecology research to conservation and evolutionary biology, obtaining a highly contiguous, extremely accurate genome is key to answering your important questions. Which genes are involved in plant growth? What do the genomes of related species reveal about their evolution?  How can genomics improve your breeding program? Why is a certain plant vulnerable to a disease?  
We can help you answer these and other questions about plants and animals with Dovetail Genomics technologies and services that simplify and streamline the creation of reference genomes.

The path to a high-quality genome assembly can start wherever is best for you.
We can begin by creating a draft assembly with the ideal sequencing technology for your organism, or by using a draft assembly you've already created. 
Next, we generate and prepare proximity ligation libraries using either our Chicago® or Dovetail™ Hi-C services.
Finally, we use our 
HiRise™ software platform to provide order, orientation and increasing contiguity up to chromosome-level. Our genome assembly services are flexible, and we will work with you to choose the best solution to meet your research goals.  
In just weeks, you'll have a complete reference genome that is highly contiguous, highly accurate, and ready to provide vital insights for your research.

You can also bring the technology of the Dovetail™ Hi-C service to your own lab.  
Prefer a more hands-on approach to your research? We have you covered. Our new Dovetail™ Hi-C Library Preparation Kits are run in your lab, on your schedule, with your sequencers.

Product List


Case Study - Plantain Genome Enhances Food Security


Chicago® improves order, orientation and contiguity of fragmented de novo assemblies and corrects errors in highly contiguous assemblies to produce a more accurate genome assembly that is optimal for scaffolding up to chromosome level with Hi-C.



Dovetail™ Hi-C Kits make running Hi-C in your lab easier than ever

Researchers are increasingly interested in Hi-C data, but significant challenges remain to establishing and maintaining a Hi-C assay in a lab. Available Hi-C protocols are time-intensive and have historically required substantial troubleshooting. The Dovetail™ Hi-C Library Preparation kit has been optimized through Dovetail's in-house Hi-C service. The kit comes with the reagents needed to create Illumina® sequencing-ready libraries. The protocol is extremely robust. In a validation study 100% of samples generated high-quality Hi-C sequencing libraries. The protocol has also been optimized to simplify and shorten the work flow, supporting sample to sequencing-ready library in just 2 days, greatly reducing the obstacles to running the Hi-C assay in your lab.

Dovetail™ Hi-C kit and HiRise™ software are integrated and optimized for genome assembly

The best approach for generating high-quality assemblies is optimizing the molecular biology technique and scaffolding software together specifically for genome assembly. Until now, for the Hi-C data type, there were no integrated, optimized and commercially available genome scaffolding solutions for the lab. Dovetail, through its services group, has actively optimized the Dovetail™ Hi-C molecular biology protocol and HiRise™ pipeline with more than a 1000 genomes scaffolded to date. The integrated and optimized Hi-C assembly service has been encapsulated into the Dovetail™ Hi-C library preparation kit and HiRise™ software now directly available to labs.


  • Capture Megabase range information with Dovetail's proximity ligation technology
  • Generate chromosome-level assemblies with HiRise™, the leading proximity ligation genome scaffolding software
  • Dovetail quality assemblies in your lab; optimized end-to-end from the world's leading service
  • Makes running Hi-C in your lab easier than ever with robust sequencing-ready libraries and high quality Hi-C data
  • Assemble more genomes to answer more biological questions with a lower cost per sample, on your own schedule
  • The convenience of a single kit for all genomes from plants to a wide variety of animals



HiRise™ assembly software scaffolds up to whole chromosomes with high confidence.

Dovetail™ Hi-C generates proximity ligation data that links regions of a chromosome together ranging from hundreds of bps to Mbps apart. The HiRise™ software is built on a statistical model that takes into account the unique read pair separation distribution of this data.

Initially, HiRise™ aligns Dovetail™ Hi-C data to scaffolds of the existing draft assembly and generates a custom statistical model based on the read-separation distribution of the Hi-C data. The software then scans through the draft assembly for errors, then breaks and rejoins the scaffold when an error is identified. HiRise™ iterates over many candidate arrangements to produce a better scoring assembly, then refines the likelihood model for additional rounds of scaffolding improvement. The pipeline repeats this process until it produces the most confident arrangement of scaffolds supported by the data.

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