This repository contains the essential files for creating a nextstrain build for running and visualizing phylogeographic analyses of pathogen spread using genomic data.
Keep the Author and License sections, and edit the rest of this README file as you wish, creating a description of your project using the GitHub Markdown, with topics and subtopics.
Native Linux and Mac Users are all set, and can move on to step #2. Windows users, however, must install a Linux subsystem before being able to install nextstrain. Visit this website and follow its step-by-step guide about how to setup Linux on Windows (please choose 'Ubuntu 18.04 LTS'), and how to launch Linux and create a user account and password on command line.
Familiarize yourself with basic UNIX commands for navigating and managing files and folders in a command line interface (Terminal). In this environment you can perform all simple tasks you usually do using mouse clicks: copy, move, delete, access, and create files and folders. All you need to do is to type a few commands. Below you can find the main commands required to operate in a Terminal. Please access this page to learn a few more commands. Please practice their use before the class, so that you are able to navigate from/to directories ("folders") and manage files and folders in command line interfaces.
| Creating, Moving and Deleting | Navigating directories | Checking content |
|---|---|---|
| mkdir folderX → create folderX | cd folderX → move into folderX | ls → list files and folders |
| mv → move files/folder from/to another directory | cd .. → go back to previous folder | head → see the first 10 lines of a file |
| rm → delete files/folders from a directory | pwd → check you current directory | tail → see the last 10 lines of a file |
Click here to download the guidelines to install nextstrain. That document provides instructions on how to install augur (bioinformatics pipeline) and auspice (visualization tool). For more information concerning installation, visit this nextstrain page for
Click here to download the course handout with a step-by-step tutorial on how to prepare your working directory (files and folders), run augur, and visualize the results with auspice. Please check this webiste for more information about the distinct functionalities of nextstrain.
- Anderson Brito & Grubaugh Lab - Website - [email protected]
This project is licensed under the MIT License.