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Robert J. Gifford edited this page Oct 23, 2024 · 33 revisions

Welcome to the Dengue-GLUE User Guide!

Dengue-GLUE is an open resource supporting comparative genomic analysis of dengue virus (DENV), developed using the GLUE software framework.

Dengue virus (DENV) is a mosquito-borne flavivirus. DENV infection causes dengue fever, an endemic disease in tropical and subtropical regions worldwide.

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. Users can interact with project data via GLUEs command line interpreter and scripting layer. This foundation supports systematic comparative analyses and the development of sequence-based resources.

Key Features

  • Comprehensive Database: Dengue-GLUE integrates DENV genome feature definitions, genome-length reference sequences, multiple sequence alignments, and standardised metadata for all DENV lineages.

  • 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: Dengue-GLUE can be used for exploratory work in a research setting, but can also provide a robust foundation for more operational processes (e.g. to be performed in a public health setting).

  • Extensible 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.

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 and Install the Dengue-GLUE 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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