Chicago™ + HiRise™ Service

Chicago – increase assembly contiguity and accuracy



High-quality de novo assembly and scaffolding for plants, animals, and bacteria has never been easier, faster, or more affordable. Using our proprietary Chicago in vitro proximity ligation method we’ll create a library from any DNA source 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 Chicago + HiRise Service Process – 6 to 10 Weeks

HMW DNA Extraction

Dovetail extracts high-molecular-weight (HMW) DNA from customer-provided sample or verifies quality of customer-provided DNA. Samples may include:

  • Animal tissue: 500 mg, freshly collected and flash-frozen, preferably cell-dense (e.g. liver, blood, brain).
  • Plant tissue: 5 g, freshly collected and flash-frozen, preferably young tissue (e.g. new leaves).
  • HMW DNA: 2 µg, 100 ng/µL, minimum mean fragment size of 50 kbp, 100+ kbp preferred.
De Novo Assembly with Illumina or PacBio Sequencing

Before Dovetail’s Chicago 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.
Chicago Library Prep

Chicago 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 DNA length measurement.
  • Calculating the amount of sequencing required to reach desired physical coverage levels.
Chicago Sequencing

Sequencing of the Chicago 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 Chicago sequence data. Upon completion of scaffolding, customer receives:

  • The final, scaffolded assembly in FASTA format.
  • A report summarizing key assembly statistics, features of the Chicago 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 Chicago 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 Chicago + 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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