Dovetail™ Hi-C + HiRise™ Service

Dovetail Hi-C – maximize assembly contiguity up to the length of full chromosomes



High-quality de novo assembly and scaffolding has never been easier, faster, or more affordable. Using our proprietary Dovetail Hi-C method we’ll create a library from any organism that can be sequenced on any modern sequencing platform. Then we’ll use our HiRise™ software to quickly, easily, and affordably scaffold your de novo assembly.



The Dovetail Hi-C + HiRise Service Process – 8 to 10 Weeks

Sample Prep

Dovetail uses endogenous chromatin as input into the Dovetail Hi-C method. Samples may include:

  • Animal tissue/blood
  • Plant tissue
  • Cell culture

De Novo Assembly with Illumina or PacBio Sequencing

Before Dovetail Hi-C generated libraries can be produced and checked for quality, a draft genome assembly must be procured. There are three options for obtaining a draft assembly:

  • Most comprehensive: Dovetail produces an Illumina or PacBio input assembly:
    • Illumina: Dovetail generates and sequences Illumina shotgun libraries to ~80x sequencing coverage of genome and performs conventional de novo assembly using Meraculous.
    • PacBio: Dovetail generates SMRT® libraries, sequences them to 50-100x sequencing coverage of genome, and assembles PacBio reads with Falcon. (*PacBio assembly adds additional time to the project timeline)
  • Save on data collection:
    • Illumina: Customer provides Dovetail with ~80x sequencing coverage of conventional shotgun data, and Dovetail performs conventional de novo assembly using Meraculous.
    • PacBio: Customer provides Dovetail with 50-100x sequencing coverage of PacBio data, and Dovetail constructs an input assembly using Falcon.
  • Quick start: Customer provides Dovetail with an input assembly.
Dovetail Hi-C Library Prep

Dovetail Hi-C generated libraries are prepared and QC’d using the draft de novo assembly. QC entails:

  • Ensuring libraries contain sufficient complexity.
  • Ensuring insert distribution meets expectations from lab measurement.
  • Calculating the amount of sequencing required to reach desired physical coverage levels.
Dovetail Hi-C Sequencing

Sequencing of the Dovetail Hi-C generated library may be performed by Dovetail, one of Dovetail’s service providers (fastest), or by a customer-selected sequencing facility (most cost-effective).

Scaffold: De Novo + HiRise

Dovetail performs scaffolding with its HiRise software pipeline. Inputs to the pipeline are the draft de novo assembly, shotgun data, and the Dovetail Hi-C sequence data. Upon completion of scaffolding, customer receives:

  • The final, scaffolded assembly in FASTA format.
  • A report summarizing key assembly statistics, features of the Dovetail Hi-C library, and the improvement over the input assembly.
  • A table of putative misjoins that were broken in the input assembly.
  • A table mapping input contigs/scaffolds to final scaffolds.
  • Alignments of the Dovetail Hi-C read pairs to the input (draft) assembly.

We take great pride in our collaborative approach and the positive customer experience we provide.  If difficulties are encountered, we will immediately provide a summary of the challenges and then find a solution that will move the project forward.

Getting started

To learn more about what our Dovetail Hi-C + HiRise Service can do for you, email us at, call 1.831.713.4465, or fill out and submit this form.


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