For this analysis (and coding in general) you will need to ensure you computer has a few things installed.
This will depend on your operating system and of course what interfaces you intend to use.
The documentation below is largely from Software Carpentry
The Bash Shell Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
Windows
cmd and press [Enter])setx HOME "%USERPROFILE%"exit then pressing [Enter]This will provide you with both Git and Bash in the Git Bash program.
macOS
The default shell in all versions of macOS is Bash, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.
Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).
You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don’t have one already. Please consider what personal information you’d like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.
Windows
Git should be installed on your computer as part of your Bash install (described above).
macOS
Video Tutorial For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent “mavericks” installer from [this list]. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled “snow-leopard” available here.
When you’re writing code, it’s nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on macOS and Linux is usually set to Vim, which is not famous for being intuitive. if you accidentally find yourself stuck in it, try typing the escape key, followed by :q! (colon, lower-case ‘q’, exclamation mark), then hitting Return to return to the shell.
Windows
Video Tutorial nano is a basic editor and the default that instructors use in the workshop. To install it, download the Software Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection.
Others editors that you can use are Notepad++, atom or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.
macOS
nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.
Others editors that you can use are Text Wrangler, atom or Sublime Text.
R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.
Windows
Video Tutorial Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select “Run as administrator” instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.
macOS
Video Tutorial Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.
Recommendation R is much more than statistics, and making graphs, it is a never-ending tool that is constantly being updated. Before we know it R will be able to cook your dinner and go to the shops too! But for now check out its great range of features for project management. It can talk all types of coding languages, and is useful to keep track of exactly what you are doing. You can even make your own webpage to help keep track of all that code and information, just like I am doing here! Some links to get you started: - R markdown - R shiny - R project for statistical computing - Project management with RStudio - R bookdown
Although Jupyter notebook is not neccessary to run the NGS analysis outlined in this webpage it is a very useful, easy to use and well documented tool. I have played around with both and I always seem to go back to RStudio + command line (MacOS), but take your pick!
It combines all the tools above - such as Bash and R and includes a lot more. It is great if you are interested in python scripting. In addition it also gives you an anaconda environment which is a common requirement for some program (in this case QIIME2). It can serve as a ‘one stop shop’ in respect to being able to execute Bash and Python code, it allows easy install of dependencies (which is partiuclarly prevelent in Python language) it allows you to use markdown with ease, and integrates with github. RStudio and a number of other programs are also integrates into the anaconda environment.
For download of Anconda - Jupyter notebook click here.
A good (but perhaps long) video tutorial is available here.
See the usearch getting started page for information on installing and excuting commands using USEARCH.
The QIIME2 native install page will get you started for your QIIME analysis.
The pages on RStudio, starting with Phyloseq Intro will walk you through any additional RStudio packages you will need.
Vector and Waterborne Pathogens Research Group. 2018. S Egan.