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Robert J. Gifford edited this page Dec 21, 2024 · 4 revisions

AAV Atlas

Welcome to the AAV-Atlas wiki!

AAV-Atlas is a sequence-oriented resource for comparative genomic analysis of adeno-associated viruses (AAVs), developed using the GLUE software framework, and tailored for genomic analysis of adeno-associated viruses (AAVs).

Key Features

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

  • Phylogenetic Structure: Sequence data in AAV-Atlas is organized in a phylogenetically-structured manner, allowing users to explore evolutionary relationships comprehensively.

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

  • Automated Genotyping: Includes functionality for assigning AAV sequences to groups and subgroups using maximum likelihood clade assignment (MLCA).

  • Variant Mapping Maps amino acid substitutions across all published AAV sequences, facilitating comparative analysis.

AAV Atlas

Overview

  1. Home
  2. Background
  3. Utilising AAV Atlas

Installation & Usage

  1. Requirements
  2. Docker Installation
  3. Native Installation
  4. Usage Overview

Project Documentation

  1. AAV Atlas Overview
  2. Schema Extensions

The 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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