Norovirus Phylogenetics Pipeline

This is a bioinformatics pipeline for building interactive norovirus phylogenetics trees that can be visualized using the Augur / Nextstrain / Auspice workflow.

Norovirus Phylogenetics Pipeline

This Nextflow pipeline implements a series of bioinformatics analyses for Norovirus phylogenetics using the Augur toolkit.

Analyses Performed

The pipeline performs the following analyses:

1. Sequence concatenation / filtering
2. Sequence alignment
3. Phylogenetic tree construction
4. Tree refinement
5. Ancestral state reconstruction
6. Sequence translation
7. Data export for visualization

Pipeline Workflow

graph TD
    A[Input Sequences] --> C[align]
    C --> D[tree]
    D --> E[refine]
    E --> F[ancestral]
    F --> G[translate]
    E & F & G --> H[export]
    I[Reference] --> C
    J[Metadata] --> E
    K[Reference Annotation] --> G
    L[Config Files] --> H

Loading

Usage

To run the pipeline, use the following command:

nextflow run BCCDC-PHL/noro-phylo-nf -r 0.1.0 --sequences /path/to/multi.fasta --outdir /path/to/output --reference /path/to/reference.fasta --run_name test1

Parameters:

• --sequences for a single multi-FASTA file
• --outdir: Output directory
• --reference: Path to the reference genome file
• --metadata: Path to metadata file (optional)
• --reference_annotation: Path to reference annotation file (required if reference is not in GenBank format)
• --config_auspice: Path to Auspice config file
• --config_colors: Path to colors config file
• --config_lat_long: Path to latitude/longitude config file

Output Files

File Name	Description
aligned.fasta	Multiple sequence alignment
tree.nwk	Phylogenetic tree in Newick format
tree.refined.nwk	Refined phylogenetic tree
branch_lengths.json	Branch length information
traits.json	Reconstructed trait data
nt_muts.json	Nucleotide mutations
aa_muts.json	Amino acid mutations
auspice.json	JSON file for visualization in Auspice

Dependencies

This pipeline requires:

• Nextflow
• Augur toolkit
• Other bioinformatics tools (as specified in the Nextflow config)

Contact

• John Palmer
• [email protected]