The ability to conduct bioinformatic analyses depends in large part on understanding how to navigate within a Unix environment. This tutorial provides an introduction to shell scripting and other basics needed to achieve independence in your bioinformatics journey.
"The Unix shell has been around longer than most of its users have been alive. It has survived so long because it’s a power tool that allows people to do complex things with just a few keystrokes. More importantly, it helps them combine existing programs in new ways and automate repetitive tasks so they aren’t typing the same things over and over again. Use of the shell is fundamental to using a wide range of other powerful tools and computing resources (including “high-performance computing” supercomputers). These lessons will start you on a path towards using these resources effectively."
The following workshop introduces the challenges and avenues for handling amplicon or shotgun metagenomic data in light of its inherent compositional nature. Led by Dr. Justin Shaffer, Gibraan "Gibs" Rahman , Lisa Marotz, Cameron Martino, and Merhbod Estaki of the Knight Lab at the University of California San Diego
Time Stamps (Hour)
(1-2) Introduction to composionality (Mehrbod Estaki & Justin Shaffer)
(4-5) Compositional time series and spatial analyses (Cameron Martino)
(5-6) Parameterizing Songbird, introduction to BIRDMan (Gibraan Rahman)
Introduction to Shotgun Metaganomic Analyses
This series provides an excellent introduction to concepts and analytical methods for processing shotgun metagenomic data, produced by the Meren Lab at the University of Chicago