Mike the Mad Biologist points to a nice article that describes aspects of the next-generation sequencing technologies with some helpful animations to illustrate the different styles. Mike goes on to describe that the sequencing itself isn’t the rate limiting step–the assembly and analysis steps are the hurdles really.
The dust certainly hasn’t settled on the strategies for that at this time–and as Mike describes the challenges may vary by species, but we are keeping an eye on some of the software that is being used (see Next-gen sequencing issue in Bioinformatics and Curious about short read sequencing? among others here).
This data is turning up in databases now (see this ENCODE data at the UCSC Genome Browser as just one example), and will continue to flood in at dramatic rates. And the same technologies are being used for analysis of other aspects of biology (not just sequencing new species and individuals)–such as promoter binding or nucleosome positioning or RNA protein binding. So it is worth taking a look at the underlying technology to understand what’s being sequenced.
and the Wellcome Trust article he describes is: Genomics – the next generation