Ion Torrent technology is a good option for many projects depending on factors like cost and time and, of course the goal of the project.
In Era7 bioinformatics we have experience analyzing data from Ion Torrent machines like for example, the first draft of the E. coli genome from the German outbreak.
BGI released the 2 of June of 2011 the German outbreak E. coli genome using IonTorrent technology to obtain very quickly a first draft of the genome:
Although this draft had more than 3000 contigs , thanks to our bacterial genome annotation system BG7 (PLOS ONE publication about BG7 ) that is specially designed for NGS data, we released the first annotation of the E. coli genome on 3 of June of 2011.
Ion Torrent PGM is being increasingly used in many labs
Specially for amplicons. It has a fast run time and a very affordable price.
The new machine Ion Proton is already in use in some labs
Ion Torrent company says that Ion Proton is specially designed for genomes.