Our first content filled meeting of the year was all about sequencing technologies. How they work, what you get from them, and how to choose among them.

There are many good papers about this topic, but we focused on three:

Sequencing Technologies, the Next Generation (Metzker, 2010)

Field guide to next-generation DNA sequencers (Glenn 2011)

(The field guide is extra useful because the time-sensitive figures are updated each year and available here.)

Ten years of next-generation sequencing technology (van Dijk, 2014)

These papers all provide multiple comparisons of the many current sequencing technologies, from nearly every conceivable angle. Highlights from these papers, and a presentation covering the chemistry of several sequencing technologies is available on Figshare.

Much of the discussion focused on the physical way in which different sequencing is done while highlighting some of the advantages and disadvantages of the techniques. In addition to talking about how sequencing works, we looked at a few files that come out of sequencing projects. To do this, we used a NGS tutorial that is available on Github.

Sequencing files are often very large, and often will not open in programs like Word, or even a plain text editor. Instead, we have to interact with them via the command line. The tutorial linked above helps you to understand the structure of several common sequencing output files by interacting with them using simple command line tools. If you end up using the tutorial, and find any errors, or have any problems, please comment below, I’m always updating my tutorials to make them more user friendly.

It was not part of this class, but the last thing I want to mention is that at 6pm on the first Tuesday of each month I’ll be hosting a practical session on NGS computing. If you’re interesting in attending, please sign up on our Google group. On October 6th, we’re doing an Intro to R.