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Robert J. Gifford edited this page Sep 24, 2024 · 33 revisions

Welcome to the Dengue-GLUE User Guide!

Dengue-GLUE is a sequence-oriented resource for comparative genomic analysis of dengue virus (DENV), developed using the GLUE software framework.

GLUE is an open, integrated software toolkit designed for storing and interpreting sequence data. It supports the creation of bespoke projects that incorporate essential data items for comparative genomic analysis, such as sequences, multiple sequence alignments, genome feature annotations, and other associated data. Projects are loaded into the GLUE "engine," forming a relational database that represents the semantic relationships between data items. This foundation supports systematic comparative analyses and the development of sequence-based resources.

Dengue-GLUE contains DENV feature definitions, alignments, and reference sequences for all DENV serotypes and genotypes, as well as all major and minor lineages defined here. Additionally Dengue-GLUE contains functionality for likelihood-based genotyping of DENV sequences, following recently developed standard nomenclature.

This Dengue-GLUE base project can be extended with additional layers, openly available via GitHub. These include NCBI-Dengue-GLUE: which extends Dengue-GLUE through the incorporation of all DENV sequence data published in NCBI GenBank.

Key Features

  • GLUE Framework Integration: Built on the GLUE software framework, Dengue-GLUE offers an extensible platform for efficient, standardized, and reproducible computational genomic analysis of dengue virus.

  • Phylogenetic Structure: Sequence data in Dengue-GLUE is organized in a phylogenetically-structured manner, allowing users to explore evolutionary relationships easily.

  • Rich Annotations: Annotated reference sequences enable rigorous comparative genomic analysis related to conservation, adaptation, structural context, and genotype-to-phenotype associations.

  • Automated Genotyping: Dengue-GLUE can perform automated genotyping of DENV sequences (including subgenomic sequences) following recently proposed lineage nomenclature, via GLUE's maximum likelihood clade assignment (MLCA) algorithm.

  • Exploratory and operational: The GLUE framework allows sequence-based resources to be used for exploratory work in a research setting, as well as more operational processes performed in a public health setting.

Getting Started

To begin using Dengue-GLUE for comparative genomic analysis, follow these steps:

  1. Install GLUE: First, install the GLUE software framework, which forms the foundation of Dengue-GLUE. You can either opt for a native installation or use Docker, depending on your preferences and system setup.
  2. Download the Dengue-Project: Once GLUE is installed, download the Dengue-GLUE project, which contains the essential parvovirus sequences, annotations, and alignment data.
  3. Create the Project: Dengue-GLUE can be installed as prebuilt database, or constructed from scratch via a local project build process. The prebuilt database allows for quick setup, while the local build process allows for more customization.

Dengue GLUE

Overview & Installation

  1. Home
  2. Background
  3. Requirements
  4. Native Installation
  5. Docker Installation
  6. Usage

Dengue Core Project

  1. Database Schema
  2. Project Data

Dengue NCBI Extension

  1. Install Options
  2. NCBI Project Data

Usage

  1. Interacting with Dengue-GLUE
  2. Sequences
  3. Alignments
  4. Serotype Recognition
  5. Genotyping Tools
  6. Mutation Frequencies

External Reference

  1. Dengue Lineages Project

The GLUE Framework

User Guide

  1. Project Data Model
  2. Schema Extensions
  3. Modules
  4. Alignments
  5. Variations
  6. Scripting Layer
  7. Freemarker Templates

Command Reference

  1. Command Mode Reference
  2. Mode Non-Specific Commands
  3. Module Type Reference
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