Visualizing Your Results Using the RIVET Frontend

Install

Make sure you have installed the RIVET frontend on your machine before proceeding. The installation steps can be found here: Install RIVET On Your Machine

Note

If you are using the RIVET frontend to visualize recombinants for pathogens other than SARS-CoV-2, please see the Using RIVET for Other Pathogens page.

Configuration

RIVET's frontend settings can be configured using the provided YAML file, config.yaml.

# Configuration file for RIVET
### Color Schema Options ####
# Base coloring
a: '#cc0000'
g: '#cc7722'
c: '#57026f'
t: '#338333'
base_matching_reference: '#dadada'
reference_track: '#333333'

# Recombinant-Informative Coloring for polygons/position column labels
recomb_match_acceptor: '#2879C0'
recomb_match_donor: '#F9521E'
non_informative_site: '#dadada'

# Breakpoint Intervals
breakpoint_intervals: '#800000'

# Genomic Coordinate Track (default all genomic regions are same color)
genomic_regions: '#33333'
# Step for tick-marks on genomic coordinate track
tick_step: 1000

# Pathogen
ref_seq: NC_045512.gb

### Taxonium Tree View Options ###
date: 2023-01-31
bucket_name: public_trees

# Keep environment as "local"
environment: local
# If running locally, port to use
port: 2000

Warning

When running RIVET locally, don't change the environment field. Also, it won't be necessary to change the date field or bucket_name field.

Run the following command to launch the RIVET frontend in your local browser.

Example

Try the following example using example SARS-CoV-2 recombinants provided in the example/ directory.

python3 rivet-frontend.py -r example/final_recombinants_example.txt -v example/trios_example.vcf -c config.yaml

Required Inputs

-f, RECOMBINANT_RESULTS: Input text file containing inferred recombinant nodes. First three columns in this text file must contain (1) recombinant node ID\t (2) donor node ID\t (3) acceptor node ID. Note, donor and acceptor denote the two parental nodes of the inferred recombinant.

Expected format:

Recombinant Node ID	Donor Node ID	Acceptor Node ID
node_1156861	node_1155169	node_1167556
node_1067629	node_1021823	node_1156861

Additional columns can be provided optionally and will be included in the rendered results table, but are not required.

Note

The RIVET backend will automatically generate the necessary input files above. Follow the steps listed on the Inferring Recombinants Using the RIVET Backend page. However, the RIVET frontend can also be used independently of the backend, just ensure that the input files adhere to the expected formatting.

-v, VCF: An input VCF containing single-nucleotide variants (SNVs) of all recombinant/donor/acceptor trio nodes present in the input RECOMBINANT_RESULTS file.

Note

RIVET only supports viewing single-nucleotide variants (SNVs), and not indels or SVs. Please see the following workflow to create a VCF for uploading to RIVET locally.

-c, CONFIG: The config.yaml file, shown at the top of this page, and provided in the repository.