Assembly Scaffolding Service

Catalog # 20011

Assembly Scaffolding Service

Catalog # 20011

A highly contiguous genome assembly is critical for efficient and accurate downstream analyses. Improve the contiguity of any existing genome assembly with scaffold N50 > 100 kb using Dovetail® Omni-C® scaffolding technology and HiRise® software. Unlike traditional Hi-C methods that utilize a restriction enzyme(s), Omni-C digests chromatin using a sequence-independent endonuclease for even, unbiased whole genome coverage. HiRise is our industry-leading scaffolding software that we have used to assemble genomes of >1,800 species. Industry-leading software accuracy coupled with manual correction by a qualified bioinformatician will get you a chromosome-scale assembly you can trust.

Why Use Our Assembly Scaffolding Service?

For the vast majority of genomes, long-read sequencing is insufficient to yield a chromosome-scale assembly. Increase the contiguity of your assembly up to chromosome-scale with Omni-C restriction enzyme-free proximity ligation and HiRise software. You’ll get:

  • Full service from sample to scaffolded assembly.
  • Unbiased DNaseI-based chromatin digestion for even whole genome coverage.
  • Manual correction for optimal accuracy.
  • Dedicated project manager for pre- and post-project support.

How It Works

Ship us a flash-frozen tissue sample and upload your existing assembly with scaffold N50 >100kb. A qualified bioinformatician will check the assembly for accuracy and completeness. If your assembly passes our QC thresholds, a dedicated project manager will set up your scaffolding project.

We will construct Omni-C proximity ligation libraries, QC the libraries, deep sequence with Illumina PE 150, and scaffold using HiRise®. Topologically associated domains (TADs) will be reported if present. A detailed project report will accompany your high quality, chromosome-scale assembly. Post-project discussion with your project manager is available upon request.

Eastern Quoll

Eastern Quoll

For our conservation genomics project, we provided Dovetail with a precious and limited sample from our species of interest. We were blown away by the completeness and of the chromosome-scale assembly they produced using HiFi, Omni-C, and the HiRise pipeline. With an assembly drastically exceeding Vertebrate Genomes Project standards in hand, we can put all our focus on the downstream science.

– Charles Feigin, Princeton University

Specifications

Delivery Time Inquire
Sample Requirements An input draft assembly with >100 kb scaffold N50 and most contigs over 1Kb, a tissue or DNA sample of sufficient quality, and any species-specific information (e.g. estimated genome size).
Library Dovetail Omni-C Library
Sequencing Platform Illumina
Analysis Platform HiRise (scaffolding)
Project Deliverables HiRise Assembly deliverables: 

  • The HiRise assembly in FASTA format
  • A report summarizing key assembly statistics, features of the Omni-C library, and a linkage density plot of the proximity ligation library data
  • A table detailing the breaks made to the input scaffolds
  • A table describing the position of the input assembly scaffolds within the final HiRise
  • BAM file(s) containing alignments of the Omni-C library read pairs mapped to the draft assembly
  • QC report
  • Raw ILMN data from deep sequencing the Omni-C library

TAD Analysis deliverables, if applicable, include:

  • TAD calls at 10 kbp, 25 kbp, and 50 kbp
  • CTCF binding sites
  • A/B compartmental organization
  • Isochore locations
  • Guide to loading and viewing in HiGlass
  • Summary report

Resources

Case Studies

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Tree of Life

Technical Information

Scientific Literature