This repository provides the data and scripts associated with the tutorial for creating a phylogenetic workflow with VCF input. The tutorial uses Mycobacterium tuberculosis sequences as an example.
The workflow encompasses preparing data for analysis, doing quality control, performing analyses, and saving the results in a format suitable for visualization (with auspice). This involves running components of Nextstrain such as augur and auspice.
Follow the standard installation instructions for Nextstrain's suite of software tools.
Run the default workflow via:
nextstrain build .
nextstrain view .
This repo is an exact copy of the Nextstrain tb workflow at this point: https://github.com/nextstrain/tb/tree/dd3ef8a08eca138a0e4e8c26b3b34dc9c4d83139
The repo was created through the following process:
- Creating a mirror of the tb repo https://github.com/nextstrain/tb.git
- Renaming
north-america-archivedtomainand setting it as the default branch - Deleting all other branches