giffordlabcvr/hbv-glue

A GLUE project for hepatitis B virus (HBV).

HBV-GLUE: Phylogenomic Analysis of Hepatitis B Virus

Overview

HBV-GLUE is a sequence-oriented resource for comparative genomic analysis of hepatitis B virus (HBV), 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, incorporating 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.

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

It can be extended with additional layers, also openly available via GitHub, including:

• NCBI-HBV-GLUE: extends HBV-GLUE through the incorporation of all HBV sequence data published in NCBI GenBank.
• HBV-DRUG-RESISTANCE : a drug resistance-focused extension incorporating an analysis tool that provides genotypic assessment of drug resistance/susceptibility.
• HBV-GLUE-WEB: a web interface that can be used to create a HBV-GLUE web-server.

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

Table of Contents

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

Key Features

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

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

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

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

• Automated Genotyping: HBV-GLUE can perform automated genotyping of HBV 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 HBV-GLUE sequence database, and provides web access to an in-built sequence analysis tool (provides genotyping, analysis and visualisation of submitted FASTA sequences).

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

Installation

If you have not done so already, install the GLUE software framework by following the installation instructions on the GLUE web site:

Note the HBV-GLUE project has a layered structure. This approach simplifies project management because it allows data items that are likely to be used across a wide range of analysis contexts to be maintained separately from those only required for more specialized purposes. The ‘base’ layer of HBV-GLUE contains only a minimal set of essential data items required for comparative analysis. This layer can be extended by adding the NCBI-HBV-GLUE extension, which incorporates all HBV sequences in NCBI GenBank and their metadata.

Prebuilt versions of HBV-GLUE can be downloaded here.

Alternatively, you can build the project locally. To do this, download the HBV-GLUE repository, navigate into the top-level directory, and start the GLUE command line interpreter, e.g.:

rob$ gluetools.sh

GLUE Version 1.1.107
Copyright (C) 2015-2020 The University of Glasgow
This program comes with ABSOLUTELY NO WARRANTY. This is free software, and you
are welcome to redistribute it under certain conditions. For details see
GNU Affero General Public License v3: http://www.gnu.org/licenses/

Mode path: /
GLUE>

At the GLUE command prompt, run the 'buildCoreProject.glue' file as follows:

GLUE> run file hbvProject.glue

Usage

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.

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

Contributing

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

License

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

Contact

For questions, issues, or feedback, please contact us at [email protected] or open an issue on the GitHub repository.