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Influenza viruses are known for causing seasonal epidemics of respiratory disease worldwide. Their ongoing evolution presents a significant public health challenge due to the emergence of new strains capable of causing seasonal outbreaks or even pandemics.
Flu-GLUE is an open resource supporting the comparative genomic analysis of influenza viruses, developed using the GLUE software framework. This resource facilitates the study of influenza A virus (IAV), influenza B virus (IBV), influenza C virus (ICV), and influenza D virus (IDV), emphasizing collaborative research through decentralized data sharing.
Traditional approaches to influenza genome data analysis often rely on centralized repositories, which follow a 'hub-and-spoke' model. While this model has any advantages, its downside is that it restricts collaboration, scalability, and the reproducibility of data analysis, as researchers and public health professionals tend to work in silos. This fragmentation can limit the sharing of resources and prevent researchers from fully benefiting from each other's work.
Flu-GLUE aims to addresses these issues by offering a decentralized, customizable platform that allows users to build and share localized resources.
By enabling collaboration within a distributed network, Flu-GLUE aims to foster user-driven communities that develop shared computational tools and standards. This decentralized governance model promotes direct interaction between users, enabling shared tool development and data refinement, and facilitating a dynamic approach to addressing influenza research challenges.
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Comprehensive Database: Flu-GLUE integrates influenza genome feature definitions, genome-length reference sequences, multiple sequence alignments, and standardized metadata for all major influenza lineages (IAV, IBV, ICV, IDV).
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GLUE Framework Integration: Built on the GLUE software framework, Flu-GLUE offers an extensible platform for efficient, standardized, and reproducible genomic analysis of influenza viruses.
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Phylogenetic Structure: Flu-GLUE organizes influenza virus sequence data in a phylogenetically structured manner, enabling easy exploration of evolutionary relationships among different virus strains.
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Rich Annotations: Annotated reference sequences provide rigorous comparative genomic analysis capabilities related to conservation, viral adaptation, structural context, and genotype-to-phenotype associations.
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Automated Genotyping: Flu-GLUE supports automated genotyping of influenza virus sequences (including subgenomic sequences) via GLUE's maximum likelihood clade assignment (MLCA) algorithm.
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Collaborative and Decentralized: Flu-GLUE fosters direct collaboration between researchers, moving beyond the traditional hub-and-spoke model by promoting a decentralized system for data sharing and tool development.
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GenBank Filtering Tools Integration: The inclusion of GenBank filtering tools enhances data quality and consistency, facilitating more accurate and reliable analyses.
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Extensible Resource: The core Flu-GLUE project can be extended with additional layers, openly available via GitHub, enabling customized analyses and further project-specific developments.
To begin using Flu-GLUE for comparative genomic analysis of influenza viruses, follow these steps:
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Install GLUE: First, install the GLUE software framework. You can either opt for a native installation or use Docker, depending on your system setup.
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Download and Install the Flu-GLUE Core Project: Flu-GLUE can be installed as a prebuilt database for rapid setup, or it can be built from scratch through a local project build process for more customization.
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Extend the Project as Required: The Flu-GLUE repository contains an isolate-oriented database of influenza virus sequences. All sequences and isolates have been preprocessed to validate and standardize metadata, recognize segments and perform genotyping. The isolate database can be used to selectively import publicly available sequences into your Flu-GLUE instance.
By following these steps, you can leverage Flu-GLUE to conduct comprehensive comparative genomic analyses of influenza viruses, benefiting from a collaborative, decentralized approach to data and tool sharing in the field of influenza genomics.