Greetings WS2 participants, Jerry and I have included below the instructions for installing both FDSTools and STRait Razor. If you are interested in following along and/or participating in the exercises provided, please follow the instructions below. IMPORTANT NOTE: Although both FDSTools and STRait Razor are compatible with MacOS neither of us use Macs on a daily basis and don’t have ready access to these. Thus, Windows or Linux operating systems are preferred for this workshop to ensure proper installation and usage. If neither is available, please feel free to continue with installation on your Mac; however, troubleshooting assistance may not be readily available. Sorry for any inconvenience. Installing FDSTools 2.0 Note: We will be using FDSTools 2.0 in the workshop. If you currently have FDSTools v1.x installed on your system, please read “Upgrading from FDSTools 1.x to FDSTools 2.x” at www.fdstools.nl/guide.html! • Install Python version 3.5 or higher, which can be downloaded from www.python.org. Most Linux systems come with Python3 preinstalled, or offer a python3 package which can be installed using the system's package management tools. Make sure you also install the Python package installer pip3. The installers for Windows and MacOS do this automatically. On Linux, you can install pip3 using the system's package management tools (e.g., on Ubuntu, apt install python3-pip). • FDSTools is command-line software, so you need to open a command prompt or terminal window to proceed. On MacOS and Linux systems, open the “Terminal” app. On Windows 10, right-click the Start menu button (Windows logo) and select “Command Prompt” or “Windows PowerShell” from the menu. • Run the command pip3 install --upgrade fdstools to install the latest version. • Check whether the installation was successful by running fdstools --version. If this generates the error “fdstools: command not found” (or similar), you should be able to run FDSTools with the command python3 -m fdstools --version instead. Installing STRait Razor Online Note: We will be using STRait Razor v3 (for processing fastq(s)) and the Shiny application STRait Razor Online (SRO; for visualizing and interfacing with data). While data from v2s are accepted by SRO, output (i.e., allsequences.txt) from earlier versions (i.e., v1/v2) of STRait Razor are not compatible with SRO. On MacOS, Xquartz will need to be installed from https://www.xquartz.org/ and then logout and log back in. 1) Download the package at the link below. a. https://github.com/ExpectationsManaged/STRaitRazorOnline/archive/refs/heads/m aster.zip 2) Unzip the STRaitRazorOnline-master.zip file. 3) If you don’t have R installed, install R from your mirror of choice https://www.r-project.org/ 4) If you don’t have RStudio installed, install RStudio Desktop from https://rstudio.com/products/rstudio/download/#download 5) Once you have R and RStudio installed, a few packages need to be installed. You can install these packages individually using the included STRait_Razor_Online_Installation.Rmd found in the ~\\STRaitRazorOnline-master\\ directory. 6) Once all the packages are installed, open ‘app_standalone.R’ script from the same directory as the installation RMD. .