Dovetail™ Scaffolding Project
Catalogue #: 20011
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.
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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
Software
- HiGlass
Scientific Literature
- Putnam, NH, et al. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Research 26(3), 342-50 (2016)
- Erez Lieberman-Aiden, Eerez, et al. Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome. Science 326, 289 (2009)
- Chapman JA, et al. Meraculous: de novo genome assembly with short paired-end reads. PLoS One 6(8), e23501 (2011)
- Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15), 2114-20 (2014)
Case Studies & Webinars
- Case Studies
- Webinars
- Disruptive technologies for improving disease resistance in crop plants
- Chicago® and Dovetail™ Hi-C yield chromosome length scaffolds of the Ixodes scapularis genome
- Enabling non-model organism genomics with multidimensional NGS
- The American Alligator: Genomics for Non-Model Organisms
- The Genes in the Beans: High-quality reference genomes provide tools for coffee breeding improvement