Dovetail™ Scaffolding Project

Catalogue #: 20011

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Specifications

Delivery Time

10 weeks

Library

Dovetail™ Hi-C and/or Chicago® Library

Sequencing Platform

Illumina

Analysis Platform

HiRise™ (scaffolding & TAD analysis)

Service Description

Dovetail™ Scaffolding Projects enhance your current assembly. In our state-of-the-art facility, we will work with your current input to improve order, orientation, and contiguity. Moving from library creation through HiRise™ Scaffolding with proven quality techniques we will help you unlock the potential of your genome.

  • Dovetail™ library construction and sequencing with a specialized combination of our proprietary Chicago™ or Dovetail™ Hi-C
  • Assembly informatics through scaffolding with our cutting-edge assembly pipeline and genome TAD analysis, if applicable
  • Tailored approach to scaffolding using proven methodologies
  • Designated Scientific Project Manager to answer questions and provide project guidance
  • Usable genome assembly within 10 weeks
  • Highly accurate results that have been validated by multiple technology types
  • Access to Dovetail Genomics proprietary service offerings and expertise

Chicago™ Libraries use a combination of in vitro chromatin fixation, digestion and crosslink reversal to create a library type unique to Dovetail Genomics. This library type has been shown to improve ordering, orientation and contiguity even in highly accurate assemblies.

Dovetail™ Hi-C libraries use a single restriction enzyme (DpnII) for chromatin digestion prior to proximity ligation. This library uses proven Hi-C chemistry well accepted in the genome assembly and chromatin conformation research fields.

The HiRise™ Scaffolding Pipeline uses the de novo assembly as an input. Multiple iterations are completed layering the use of the library sequencing data to provide a contiguous high-quality assembly.

When available, TAD analysis uses the data collected for the assembly creation to provide a view into chromatin 3D architecture, including topologically associated domains.

Materials & Deliverables

An input draft assembly with > 50 kb N50 and most contigs over 1Kb, A tissue or DNA sample of sufficient quality, and any species-specific information (e.g. predicted genome size).

  • Final Dovetail™ Genome Assembly
    • A manifest detailing the contents of each file included in the delivery package.
    • The HiRise assembly in FASTA format.
    • A report with summary results for the assembly
    • A table detailing the breaks made to the input scaffolds.
    • A table describing the position of the input assembly scaffolds within the HiRise scaffolds.
    • BAM files
  • TAD analysis
    • Manifest – A manifest detailing the contents of each file included in the delivery package
    • Report.html – Summary statistics of the analysis, data processing information, and instructions on HiGlass browser visualization
    • alignment.bam – File containing sequence alignment data
    • X.mcool – Multiple cooler file containing the Dovetail™ Hi-C matrix of proximity
    • X.hic – HiC contact matrix at multiple resolutions in .hic format
    • X_isochores.bedpe – Output of program which calls isochores – regions of characteristic GC content within a genome
    • X.multires – Files which can be ingested in HiGlass viewer
    • Chr_sizes.txt – Chromosome size file – first column is chromosome name and the second the size of that chromosome
    • X_AB_compartments.bedpe – A/B compartments from first Eigenvector of contact matrix
    • X_CTCF_sites.bed – Predicted CTCF binding sites using Cread
    • X_TADs_10000.bedpe – Topologically associated domain (TAD) calls using arrowhead at 10,000 bp resolution
    • X_TADs_25000.bedpe – Topologically associated domain (TAD) calls using arrowhead at 25,000 bp resolution
    • X_TADs_50000.bedpe – Topologically associated domain (TAD) calls using arrowhead at 50,000 bp resolution

Documents

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