I am in the process of teaching a course on “DNA sequence based studies of microbial diversity” (EVE 161 at UC Davis) and I thought it would be of use to some people to post about it. I have made a landing page for the course: EVE 161: DNA sequence based studies of microbial diversity
This is the post for Lecture 2 which was on “The Evolution of DNA Sequencing Methods” – or – some history of DNA sequencing.
The main reading for the class was:
I told the students to read Mardis 2013 though in the end I kind of wished I had used Mardis 2008. Also – one limitation of these papers is that they are not open access so I spent some time also looking for open access papers that reviewed sequencing technology, especially those with a focus on more modern issues in sequencing (I got some help from the Twittersphere but need to compile that information still). I found the following that seemed OK:
- Metagenomics – a guide from sampling to data analysis
- Comparison of Next-Generation Sequencing System
- Key Principles and Clinical Applications of “Next-Generation” DNA Sequencing”
This also seemed useful: Next gen sequencing for dummies to it is not open access per se.
Anyway – the basic outline for what I did in class was to cover the history of DNA sequencing with a focus on next gen sequencing. I had the following outline:
- Timeline of DNA sequencing
- Generation I: Manual sequencing (with an emphasis on Sanger)
- Generation II: Automation
- Capillary / fluorescent Sanger
- Colony picking robotics
- Generation III: Colonies not Clones
- ABI Solid
- Generation 3.5
- Ion Torrent
- Generation 4: Single Molecule Sequencing
- Oxford Nanopores (what I call mythical sequencing)
Basically I tried to cover some history and then give the students a bit of “shock and awe” with how much faster and easier and cheeper sequencing is now.
My slides are in Slideshare:
Also of possible use are the following Youtube videos