De novo Genome Assembly Service

Catalog # 20012

De Novo Genome Assembly Service

Catalog # 20012

Sometimes the fastest way to get something done is to have an expert do it for you. We’re here to help you build a full de novo assembly from scratch.

We first build a draft assembly using PacBio™ HiFi™, the most accurate long-read sequencing platform available today. This assembly is then scaffolded up to chromosome-scale using Omni-C® proximity ligation technology and HiRise® scaffolding 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. This unique combination of PacBio HiFi (accuracy) plus Omni-C (coverage) enables haplotype-resolved assembly. You’ll get two genome assemblies, one for each haplotype, providing the most comprehensive view of a diploid genome. Finally, we annotate your assembly to call and label as many genes as possible.

Why Use Our de novo Assembly Service?

Trust your project to the most experienced de novo assembly service provider in the world, with over 1,800 assemblies delivered to date.

  • Enjoy full service – from sample to publishable assembly, all under one roof.
  • Get access to the latest cutting-edge technologies: PacBio HiFi, Dovetail® Omni-C, HiRise software, and the Dovetail® Annotation Service Suite.
  • Future-proof your genome by getting a haplotype-resolved assembly. Don’t settle for half the genome!

How It Works

Just send us your flash frozen tissue sample and we will deliver a complete, highly accurate and contiguous annotated genome assembly. A dedicated project manager will keep tabs on your project at all times and be available for pre-and post-project discussions. Quality control checks at every step ensure assembly accuracy.

Experience sets Dovetail apart from the rest. Each species represents a novel assembly project – every species possesses a unique genome. However, our experience having assembled more than 1,800 species’ genomes means we typically know what to expect going into a project. Plus, we can refer to similar species we have assembled and ensure that optimal taxon-specific protocols are followed.

Brittlebush

Dovetail took what seemed like an impossible project — getting an assembly for a plant with a large, repetitive genome — and made it a reality. They collaborated with different bioinformatics groups & did additional analyses to make sure we got the best results possible.

Sonal Singhal, California State University, Dominguez Hills

Specifications

Delivery Time Inquire
Sample Requirements A tissue sample of sufficient quality, and any species-specific information (e.g. estimated genome size).
Libraries PacBio HiFi, Dovetail Omni-C
Sequencing Platforms PacBio, Illumina®
Analysis Platforms HiFiasm, HiRise, Merqury
Project Deliverables HiRise Assembly deliverables include:

  • 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 scaffolds
  • BAM files(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 data in HiGlass
  • Summary report

RNA Sequencing Library deliverables, if applicable, include:

  • Six (6) FASTQ files, each containing ~20M read pairs

Genome Annotation deliverables, if applicable, include:

  • Genome annotation file in GFF3 format
  • Predicted gene CDS sequences in FASTA format
  • Predicted gene peptide sequences in FAST format
  • Alignment files from RNA-seq and Iso-Seq data in BAM format (if evidence data is provided)
  • Repeat annotation file in GFF3 format
  • Visualization of structures of manually curated genes

Resources

Case Studies

Webinars

Tree of Life

Scientific Literature

Technical Information