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Welcome to the HCV-GLUE User Guide!

HCV-GLUE is an open resource supporting comparative genomic analysis of hepatitis C virus (HCV), developed using the GLUE software framework.

Hepatitis C virus (HCV) is a bloodborne RNA virus that primarily targets the liver, causing both acute and chronic hepatitis. Classified under the Hepacivirus genus within the Flaviviridae family, HCV is mainly transmitted through contact with infected blood. If left untreated, infection can lead to serious liver complications, such as cirrhosis and liver cancer. Direct-acting antiviral medications have dramatically improved cure rates and hold the potential to eliminate the virus entirely. However, achieving global elimination faces significant challenges

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.

Key Features

• Comprehensive Database: HCV-GLUE integrates genome feature definitions, reference genome sequences, multiple sequence alignments, and standardised metadata for all HCV subtypes and genotypes.

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

• Phylogenetic Structure: Sequence data in HCV-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: HCV-GLUE can perform automated genotyping of HCV sequences (including subgenomic sequences).

• 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.

• Extensible This HCV-GLUE base project can be extended with additional layers, openly available via GitHub. These include:

  • NCBI-HCV-GLUE - incorporates all HCV sequence data published in NCBI GenBank.
  • PHE-HCV-DRUG-RESISTANCE - incorporates an analysis tool that provides genotypic assessment of drug resistance/susceptibility.
  • HCV-NABS - an extension for analysing neutralising antibody binding sites in HCV.

Getting Started

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

1. Install GLUE: First, install the GLUE software framework, which forms the foundation of HCV-GLUE. You can either opt for a native installation or use Docker, depending on your preferences and system setup.
2. Install the HCV-Project: Once GLUE is installed, HCV-GLUE can be installed as a 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.

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