In a previous lesson, you learned how to use the bash shell to interact with your computer through a command line interface. In this lesson, you will be applying this new knowledge to carry out a common genomics workflow - identifying variants among sequencing samples taken from multiple individuals within a population. We will be starting with a set of sequenced reads (.fastq files), performing some quality control steps, aligning those reads to a reference genome, and ending by identifying and visualizing variations among these samples.

As you progress through this lesson, keep in mind that, even if you aren’t going to be doing this same workflow in your research, you will be learning some very important lessons about using command-line bioinformatic tools. What you learn here will enable you to use a variety of bioinformatic tools with confidence and greatly enhance your research efficiency and productivity.

This lesson assumes a working understanding of the bash shell. If you haven’t already completed the Shell Genomics lesson, and aren’t familiar with the bash shell, please review those materials before starting this lesson.

This lesson also assumes some familiarity with biological concepts, including the structure of DNA, nucleotide abbreviations, and the concept of genomic variation within a population.

David Molik is a PhD student in Computational Biology. David is interested in the factors that affect microbial communities’ diversity over time. David writes new software, as well as uses experimental systems. David also researches computational methods in general ecological data, specifically within Metabarcoding, which is the idea of using a single gene region to parse out which species are in a sample, working out how to associate community structure with the environment, and looking at rare and pathogenic species in large amounts of data.