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Influenza viruses are members of the Orthomyxoviridae family, known for causing seasonal epidemics of respiratory disease worldwide. The segmented genomes of these viruses consist of negative-sense, single-stranded RNA. The ongoing evolution of influenza viruses 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.
Flu-GLUE promotes a decentralized model of data sharing, enabling researchers to directly share data, tools, and insights with each other. Flu-GLUE's decentralized approach fosters enhanced interaction, shared tool development, and distributed governance, accelerating discoveries and improving responses to influenza outbreaks.
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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.
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.