Accurate evaluation of the present performance of the single technologies is really difficult in a such quickly developing field as NGS...However a snapshot of the NGS technology scenario is of great advantage to everyone to evaluate which one best fit its research needs!
What's new in this paper compared to the last benchmarks from BGI (published on Journal of Biomedicine and Biotechnology) and Wellcome Trust Institute (published on BMC Genomics)?
Two competitors emerge as the leaders in the field: Ion PGM and MiSeq. Data shows data some technological and analytic gaps have been closed, with both platforms performing about the same in term of substitution detection accuracy. MiSeq performance remains better than PGM in detecting small indels (about 100-fold lower error rate), with most of the errors due to troubles in sequencing homopolymers runs. MiSeq still have the lowest cost per Mb, while PGM still the fastest and more flexible.
A good recap of the findings can be found on this post from GenomeWeb, where you can read also the first official answers from both Illumina and Life Tech.
Table from Junemann et al., Nature Biotechnology 31(4): 294-296, April 2013
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