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Robert J. Gifford edited this page Oct 14, 2024 · 28 revisions

Welcome to the Flu-GLUE wiki!

Under Construction!! (Oct 2024)

Flu-GLUE is a sequence-oriented resource for comparative genomic analysis of influenza viruses, developed using the GLUE software framework. It provides a freely accessible, public-facing platform that offers a phylogenetically-structured collection of all publicly available influenza sequence data.

Sequences from the NCBI nucleotide database are curated along with complementary sequence metadata and are integrated together using GLUE (Genes Linked by Underlying Evolution) - a data-centric software package for capturing virus sequence data and organising it along evolutionary lines.

Sequence data are richly annotated with gene features and isolate-associated information. Flu-GLUE also contains reference sequences for all influenzavirus species and subtypes, multiple sequence alignments, and clade defintions for all influenza virus segments.

Flu-GLUE

Overview & Installation

  1. Home
  2. Background
  3. Requirements
  4. Native Installation
  5. Docker Installation
  6. Usage

Flu Core Project

  1. Overview
  2. Database Schema
  3. Genome Features
  4. Sequence Data
  5. Alignment Tree
  6. Phylogenetic Trees
  7. Segment Recognition
  8. Genotyping Tools

Expanding the Dataset

  1. Background
  2. Filtering
  3. Filtering Process

Usage

  1. Sequences
  2. Alignments
  3. Mutation Frequencies

GLUE Framework

User Guide

  1. Project Data Model
  2. Schema Extensions
  3. Modules
  4. Alignments
  5. Variations
  6. Scripting Layer
  7. Freemarker Templates

Command Reference

  1. Command Mode Reference
  2. Mode Non-Specific Commands
  3. Module Type Reference
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