Nextstrain pipeline for genomic epidemiology of dengue virus (serotypes 1-4). This tool derives from flexpipe, a nextstrain pipeline developed to be flexibly adapted to any pathogen of interest (here adapted for dengue virus).
This repository contains the essential files to create a dengue virus nextstrain build. By using this pipeline users can to perform genomic epidemiology analyses and visualize phylogeographic results to track dengue virus spread using genomic data and their associated metadata.
Nextstrain panel with results overview
In order to run this pipeline for your dengue project, see instructions available on the original flexpipe repository, which provides essential information needed to navigate in Unix CLI, to install a nextstrain environment with conda/mamba, and a tutorial with detailed instructions on how to generate a Nextstrain build, which involves preparing, aligning, and visualizing genomic data.
The currently provided Snakefile is set up with parameters related to Dengue virus serotype 2, such as 5' unstranslated regions to be masked (mask_5prime and mask_3prime), evolutionary rate (clock_rate and clock_std_dev), and root method:
rule parameters:
params:
mask_5prime = 96,
mask_3prime = 451,
bootstrap = 1,
model = "GTR",
root = "least-squares",
clock_rate = 0.00078,
clock_std_dev = 0.00004,
Below are the parameters for each dengue virus serotype, which need to be adjusted within the rule parameters:
| serotype | mask_5prime | mask_3prime | clock_rate | clock_stddev |
|---|---|---|---|---|
| DenV1 | 94 | 462 | 0.00060 | 0.00004 |
| DenV2 | 96 | 451 | 0.00078 | 0.00004 |
| DenV3 | 94 | 440 | 0.00068 | 0.00004 |
| DenV4 | 101 | 384 | 0.00066 | 0.00004 |
- Anderson Brito, Instituto Todos pela Saúde (ITpS) - Website - [email protected]
This project is licensed under the MIT License.