Welcome to the Dovetail® Linked-Read Analysis Page

Dovetail® Linked-Read technology enables powerful multi-omic insight from proximity-ligated DNA, supporting a broad range of genomic applications — including variant detection, 3D genome conformation, and haplotype-aware genome assembly. This guide serves as a centralized resource for analyzing datasets generated using Dovetail Linked-Reads, integrating workflows across multiple applications and existing product-specific documentation.

Molecular Biology of the Sequence Data

The Dovetail Linked-Read assays generate proximity ligated chromatin that is then purified and converted into a sequencing library. Depending on the application, DNA can be analyzed genome-wide or enriched by protein-directed or hybrid capture-based strategies. No matter the Dovetail® product used, the sequencing data consist of chimeric molecules with insert sizes reflecting the chromatin structure in the nucleus.

Application Areas & Supporting Products

The flexible nature of these data supports multiple downstream applications through a unified experimental framework. Applications can be supported by various Dovetail® Linked-Read Products. Below is a guide to these applications and their supporting chemistries.

Workflow Overview

The general analytical workflow starts with raw FASTQ files that are aligned with standard tools to the reference genome of interest, and then filtered for valid interaction pairs. From there, users can branch into analysis workflows tailored for: • Variant Detection • Whole Genome Conformation • Targeted Conformation • Genome Assembly • Haplotype Phasing

This guide brings together these application-specific workflows in a single documentation hub, with links to detailed product-specific pages.

What’s in this guide

• Guidance on input formats and pre-processing

• Optimized data processing for workflows tailored to the Dovetail® Linked-Read Chemistries

• Application-specific documentation

• Best practices and tips for optimal data quality

Support

For help or related questions please open a new issue in the github repository or send an email to: support@cantatabio.com

Data Processing

• Before you begin
• Pre-Alignment
• From fastq to final valid pairs bam file
  • Alignment
  • Recording valid ligation events
  • Sorting the pairsam file
  • Removing PCR duplicates
  • Generate .pairs and bam files
  • Generating the final bam file
• Generating Contact Matrix
  • Generating HiC contact maps using Juicer tools
  • Generating cooler contact maps

Whole Genome Sequencing

• Quality Control & Sequencing Requirements
  • Complexity
  • QC Assessment
  • Sequencing Recommendations
• Detection of Genetic Variants
  • Structural Variants
  • Copy Number Variation
  • SNVs and Indels
• Topology
  • Feature Discovery
    • AB Compartments
    • Topologically Associated Domains
    • Chromatin Loops
  • Comparative Analysis
    • Introduction
    • Differential Analysis
• Comparative Analysis
  • Introduction
  • Differential Analysis
• Phasing
  • Compatible Tools
• Genome Assembly
  • Compatible Tools
• Datasets

HiChIP

• Quality Control & Sequencing Requirements
  • Proximity-ligation assessment
  • ChiP enrichment
  • QC Assessment
• Loop Calling
  • Introduction
  • Resolution
  • Tool landscape
  • Why FitHiChIP?
  • Input files
  • Tools
  • Workflow Overview
  • Output
  • What if?
  • What next?
• HiChIP Comparative Analyses
  • Introduction
  • Differential Analysis
• Plotting HiChIP Data
  • Introduction
  • Inputs
  • Tools and Data Used
  • Basic Workflow
  • Walkthrough
• Calling 1D peaks with MACS2 on HiChIP data
  • Introduction
  • Input files
  • Additional tools needed
  • Workflow Overview
  • Workflow
• Datasets

Capture

• Quality Control & Sequencing Requirements
  • Proximity ligation properties
  • Target enrichment QC
  • Replica Reproducibility
• Detection of DNA Looping Interactions
  • Introduction
  • Input files
  • Interaction calling
  • Output files
  • Additional suggestions for interactions data analysis:
  • For advanced users
• Capture Comparative Analysis
  • Introduction
  • Input files
  • Calling differential interactions
• Datasets