I was wondering if Shotgun sequencing was the same thing as RADseq as two methods of Next Generation sequencing. Are they also called Genotyping By Sequencing?
No they are not the same. Shotgun means random fragmentation and sequencing, in theory, all bases from your genome will be covered given enough sequencing. RADseq means restriction-site-associated DNA sequencing, and only regions surrounding restriction enzyme sites will be sequenced.
GBS may mean the original restriction enzyme associated protocol from Cornell (I think some people refer to it as Cornell GBS), or a general term which comprises several techniques. Indeed, skimGBS is a shotgun genotype by sequencing method.
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Have you tried to search with both terms? Even the respective WikiPedia pages look pretty useful.
I've looked here: https://en.wikipedia.org/wiki/Shotgun_sequencing#Next-generation_sequencing.
They are saying: "Next-generation sequencing The classical shotgun sequencing was based on the Sanger sequencing method: this was the most advanced technique for sequencing genomes from about 1995–2005. The shotgun strategy is still applied today, however using other sequencing technologies, called next-generation sequencing. These technologies produce shorter reads (anywhere from 25–500bp) but many hundreds of thousands or millions of reads in a relatively short time (on the order of a day).[16] This results in high coverage, but the assembly process is much more computationally intensive. These technologies are vastly superior to Sanger sequencing due to the high volume of data and the relatively short time it takes to sequence a whole genome.[17] "
But is it the same thing? Is it historically defined or is RAD a type of shotgun sequencing? That, I don't find it clear.