Read this first! ---------------- I teach general biology and genetics at a [community college][1]. In summer of 2019, I took a sabbatical of sorts via an ROA ([Research Opportunity Award][2]) to work in a research lab. I went to Duke University and worked in [Mohamed Noor's lab][3] to learn next-gen sequence analysis. I was disappointed in the lack of transparency and documentation in some of the programs/tools I was using, and starting writing up my own workflows and my own documentation. I include two versions of that documentation here. [One is the full version, with all the issues I ran into and all of my mistakes][4]. [The second is the clean version - no indication of any problems, just clean workflows][5]. *Note that these were written initially for other members of the Noor lab, and so may contain Duke-specific or Noor lab-specific information that is irrelevant to you.* Also note, I am not a bioinformatician. I am not a computer programmer. My lab notebooks are written for others like me. However, to use many of these tools, you will need to [learn some basic Linux][6]. I recommend doing that before starting any genomic analysis. One of the primary goals of that summer was to develop a genomics-based teaching activity, so that is also included here. This project does NOT require knowing Linux, and does not require installation of any programs - everything is run through the browser. It is intended for sophomore-level undergraduates in a Genetics course. Do I love how I've done it? No, but it's a good starting point. It contains all the instructions, so if you choose to use it, how you present it is up to you. Everything here is CC-BY licensed, which means you can download and change anything you want to fit your needs, so long as you attribute myself as the original author. Included: --------- 1. Full lab notebook of my process of learning genome analysis (linked above) 2. Clean version of the full lab notebook (linked above) 3. Image of short-read workflow using primarily tools from GATK (in files section) 4. Image of long-read workflow (in files section) 5. Sophomore-level genomics project instructions for students (in files section) 6. Summary presentation of the work I did in the Noor lab (in files section) [1]: https://centralvirginia.edu/ [2]: https://www.nsf.gov/pubs/2014/nsf14579/nsf14579.htm [3]: https://sites.google.com/site/noorlabduke/ [4]: https://docs.google.com/document/d/1wLnufiZjpwRCFVwehBhdhqUaqjFWcCE3RgSt9wkMqos/edit?usp=sharing [5]: https://docs.google.com/document/d/1oHa_rUW0xc-VZH7nTNVHEMIraAqgU1bUPLuMlTgSFSM/edit?usp=sharing [6]: https://www.codecademy.com/learn/learn-the-command-line