Example GLUE Project

GLUE Example Project: Hepatitis E Virus (HEV)

In GLUE, a project is a self-contained package containing data and analysis functions related to a specific set of virus sequences. This example project, based on Hepatitis E Virus (HEV), illustrates many of GLUE's key features.

HEV is an important cause of viral hepatitis, primarily transmitted through the fecal-oral route, especially in regions with inadequate sanitation. It is a member of the Hepeviridae family and has four main genotypes, with genotypes 1 and 2 typically associated with outbreaks in developing countries, while genotypes 3 and 4 are linked to zoonotic transmission in developed countries.

Symptoms of HEV infection include fatigue, jaundice, abdominal pain, and loss of appetite, with most cases resolving spontaneously. However, the virus can lead to severe complications, particularly in pregnant women, and chronic infection may occur in immunocompromised individuals.

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Overview

1. Download and Unpack
2. Build the Project
3. What's in the Example Project?
4. Next Steps

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1. Download and Unpack

GLUE projects conventionally store their files in dedicated directories inside the gluetools/projects directory.

Note

If you are using Docker-based GLUE, the example project is already unzipped in your container filesystem. Skip to Build the Project.

If you are using Native GLUE, download the example project zip file from the GLUE Download Page and unzip it into gluetools/projects.

Command Example:

$ cd /home/fred/gluetools/projects
$ unzip exampleProject-1.1.113.zip

Start an interactive GLUE session within the exampleProject directory:

$ cd /home/fred/gluetools/projects/exampleProject
$ gluetools.sh

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2. Build the Project

In GLUE, a project is archived as a set of files. To use it, you must build the project, which involves running commands to load project data and analysis configurations into the database.

Steps to Build:

1. Start a GLUE interactive session.
2. Execute the run file command on the file exampleProject.glue, which serves as the master build file.

Command Example:

GLUE version 1.1.113
Mode path: /
GLUE> run file exampleProject.glue
...

Troubleshooting:

• If the build reports errors (e.g., with BLAST+, MAFFT, or RAxML integrations), check the installation instructions.
• If unresolved, raise a question on the GLUE Support Forum.

A successful build ends with the output:

...
OK
Mode path: /
GLUE>

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3. What's in the Example Project?

After building, the project becomes a basic resource for storing and analyzing HEV sequences. Key elements include:

Reference Sequences and Reference Alignment

• Sequences: GenBank XML sequences are stored in ncbi-refseqs. This includes sequence L08816, used to define genome feature locations.
• Reference Sequences: ncbi-refseqs are designated ReferenceSequences as per Smith et al., 2016.
• Genome Features: Includes three ORFs and seven sub-domains of ORF1. Features from L08816 are transferred to other references via the inherit feature-location command.
• Alignment: Sequences are stored in an unconstrained alignment.

Alignment Tree and Genotyping

• Constrained Alignments: Defined for HEV genotypes and subtypes, based on ReferenceSequences.
• Alignment Tree: Links constrained alignments, with internal node homologies derived from the unconstrained alignment.
• Phylogenetic Tree: Generated using RAxML and imported into the alignment tree.
• Clade Assignment: Maximum-likelihood Clade Assignment modules allow genotype and subtype identification.

Sequence Database

• Metadata Fields: Extensions include sequence length, collection year, host species, and country of origin (based on UN M.49 standard).
• Example Sequences: Includes ncbi-hev-examples (10 GenBank XML sequences) and fasta-hev-examples (10 FASTA sequences).
• Metadata Population:
  • GenBank XML metadata is loaded using genbankXmlPopulator.
  • FASTA metadata is loaded using textFilePopulator.
• Genotyping: Example sequences are genotyped and added to the appropriate tip alignment in the alignment tree.

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4. Next Steps

Explore the Command Line Interpreter tutorial to learn how to query the GLUE project and run analyses.