Pango Network
Outbreak Investigation

Civet

Cluster Investigation & Virus Epidemiology Tool

A powerful tool for rapid SARS-CoV-2 outbreak investigation. Generate comprehensive reports with phylogenetic trees, geographic maps, timelines, and statistical summaries for epidemiological analysis.

v3.0
Latest Version
HTML
Report Format
GPL-3.0
License
Features

Comprehensive Report Generation

Civet generates interactive HTML reports with multiple visualization components for thorough outbreak analysis.

Phylogenetic Trees

Interactive trees showing relationships between query sequences and background data.

Geographic Maps

Visualize the geographic distribution of sequences in your cluster.

Timelines

Track the temporal progression of outbreaks with date-based visualizations.

Statistical Tables

Summary statistics and data tables for epidemiological analysis.

Background Context

Contextualize your sequences against known background diversity.

Custom Reports

Configurable report sections for different investigation needs.

Workflow

How Civet Works

Civet takes your query sequences and metadata, contextualizes them against background data, and generates comprehensive HTML reports.

1

Input Sequences

Provide FASTA sequences and associated metadata (dates, locations).

2

Background Dataset

Civet finds the closest matches in the background phylogeny.

3

Catchment Analysis

Defines catchment groups based on phylogenetic proximity.

4

Report Generation

Produces interactive HTML reports with trees, maps, and timelines.

Terminal
# Install civet
$ pip install phylo-civet
# Basic usage
$ civet \
-i query_sequences.fasta \
-m metadata.csv \
-b background_data/ \
-o outbreak_report/
# With CLIMB integration
$ civet \
-i query.fasta \
--CLIMB \
-o report/
# Output: Interactive HTML report
outbreak_report/
├── report.html
├── figures/
└── data/
Configuration

Customization Options

Civet offers extensive configuration options for tailoring reports to your needs.

Input Configuration

Sequence and metadata column mapping

Background Dataset

Custom or default background data

Catchment Parameters

Distance thresholds for clustering

Report Settings

Which sections to include

Map Configuration

Geographic visualization options

Timeline Settings

Date range and grouping options

Tree Visualization

Layout and annotation settings

Table Options

Column selection and formatting

Output Format

Report structure and styling

Resources

Documentation

Complete guide and tutorials

GitHub Repository

Source code and issues

Example Reports

Sample outbreak investigation reports

Citation

If you use Civet in your research, please cite:

O'Toole et al. 2021. medRxiv preprint.
https://doi.org/10.1101/2021.12.13.21267267

Start investigating outbreaks

Install Civet and generate comprehensive outbreak investigation reports.