I’ve just discovered a very promising new blog in the genomics sphere (well, technically it’s a newly relaunched blog) run by a group at the University of Birmingham.
Our reading of the situation was that Illumina have been successful because they were early to market, offered the best throughput and had a relatively simple sample preparation and data analysis pipeline. Solexa has a reputation for its decent sample preparation workflow due to its “walk away” Cluster Station machine. Solexa also produces easy to manipulate FASTQ read files which are read by all the short read mappers without the additional informatics distraction of SoLiD’s “colourspace”. Solexa has also found a way to scale rapidly from 1 gigbase per run and 36-base reads with its Genetic Analyzer 1. Now they are now routinely able to produce over 10 gigabases (and climbing) with 75-base reads and paired-ends to make analysis easier. 454 has also found a highly successful niche, particularly in bacterial applications and metagenomics, due to its longer reads, short run time and user-friendly software. SoLiD’s advantages were harder to define, sometimes characterised as “the worst of both worlds”, with a laborious sample preparation workflow, long running time, short reads and an unfamiliar output format.