HCV-GLUE is a sequence-oriented resource for comparative genomic analysis of hepatitis C virus (HCV), developed using the GLUE software framework. It includes a web interface that can be used to create an HCV-GLUE web-server.

HCV-GLUE contains HCV feature definitions, annotated reference sequences for all HCV genotypes and subtypes, and heirarchically ordered multiple sequence alignments.

This HCV-GLUE base project can be extended with additional layers, openly available via GitHub, including:

• NCBI-HCV-GLUE: extends HCV-GLUE through the incorporation of all HCV sequence data published in NCBI GenBank.
• PHE-HCV-DRUG-RESISTANCE : a drug resistance-focused extension incorporating an analysis tool that provides genotypic assessment of drug resistance/susceptibility.

A web instance of HCV-GLUE incorporating both these extension layers is hosted by the University of Glasgow, and can be accessed here.

• Overview
• Key Features
• Installation
• Usage
• Contributing
• License
• Contact

• 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: The data in HCV-GLUE is organized in a phylogenetically-structured manner, allowing users to explore evolutionary relationships easily.

• Automated Updates: HCV-GLUE provides an automatically-updated collection of HCV sequence data, ensuring users have access to the latest information for their analyses.

• Rich Annotations: Each sequence is annotated with gene features, enabling 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) using GLUE's maximum likelihood clade assignment (MLCA) algorithm, as described here.

• Web user interface: The web user interface that supports online browsing of the HCV-GLUE sequence database, and provides web access to an in-built sequence analysis tool (provides genotyping, analysis and visualisation of submitted FASTA sequences).

Please visit the HCV GLUE web page for instructions on installing HCV-GLUE.

GLUE contains an interactive command line environment focused on the development and use of GLUE projects by bioinformaticians. This provides a range of productivity-oriented features such as automatic command completion, command history and interactive paging through tabular data. Some examples are provided here.

For detailed instructions on how to use HCV-GLUE for your comparative genomic analysis, refer to the GLUE software environment's reference documentation.

We welcome contributions from the community! If you're interested in contributing to HCV-GLUE, please review our Contribution Guidelines.

The project is licensed under the GNU Affero General Public License v. 3.0

For questions, issues, or feedback, please contact us at gluetools@gmail.com or open an issue on the GitHub repository.