Dovetail™ Scaffolding Project
Catalogue #: 20011
Dovetail™ Hi-C and/or Chicago® Library
HiRise™ (scaffolding & TAD analysis)
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
- 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
- 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