Update on Next Generation Benchtop Sequencing - Strong Debut of Illumina MiSeq & Ion Torrent PGM Fastest Evolving Platform

April 05, 2013
Summary: New study ‘Updating benchtop sequencing performance comparison’ published in the Nature Biotechnology journal / MiSeq and PGM mature and affordable enough for soon application in routine epidemiologic surveillance for clinical and public health microbiology.

Since about two years affordable Next Generation Sequencing (NGS) machines with a fast turnaround time are available on the market. A team lead by the University of Münster now compared three different benchtop NGS platforms and how they evolved in the course of time. More specific the consortium comprising of researchers from the Universities of Münster and Bielefeld, Alfred Wegener Institute Bremerhaven (all based in Germany) and the Austrian University of Vienna challenged the GS Junior (Roche; Titanium 400 base [b] chemistry), MiSeq (Illumina; 2x 150b & 2x 250b paired-end consumables) and PGM (Ion Torrent; 100b, 200b, 300b & 400b kits) with bacterial whole genome sequencing. Discrepancies to a high-quality reference genome sequence were furthermore clarified by traditional bidirectional Sanger sequencing.

What the team found was that the MiSeq made a very strong official debut with only very few substitution and no insertion and deletion (indel) errors at consensus level. The GSJ had by far the lowest throughput thereby making it more costly to operate than the other two platforms. The PGM evolved rapidly in the past two years and with the newest 300/400bp chemistries this platform showed only one substitution error and a dramatic reduced number of indel errors. As these errors are systematic by nature - nearly all are related to homo-polymer stretches in the sequence - appropriate software tools can compensate for them, says the last and communicating author Dr. Dag Harmsen, a scientist from the Department for Periodontology at the University of Münster.

“The de novo assembly qualities of the MiSeq and PGM systems are amazingly good. Therefore, I expect both platforms being used routinely by early public health adopters for microbial epidemiologic surveillance to detect faster and more accurate outbreaks starting this year,” commented the medical doctor.

“To conduct a ‘fair’ NGS platform comparison is pretty hard. However, it is certainly the consensus accuracy, not the raw read accuracy, that is the relevant metric for normal end users,” explained the first author of the Nature Biotechnology publication Sebastian Jünemann, a bioinformatician from the Institute for Bioinformatics, Center for Biotechnology, Bielefeld University.

As the focus with such good and fast sequencing results is shifting away from the laboratory towards analyzing the huge amount of generated data, turnkey software tools are more than ever needed. This is exactly the topic of the EU FP7 PathoNGenTrace project where Dr. Harmsen is also involved in. “We are working on user-friendly software solutions that bridge the gap from data to knowledge and opens the door wide for routine application of NGS in clinical and public health microbiology," added Harmsen.


Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, Mellmann A, Goesmann A, von Haeseler A, Stoye J, Harmsen D (2013). Updating benchtop sequencing performance comparison. Nature Biotechnology 31(4): 294–296 / doi:10.1038/nbt.2522.

PLEASE LINK TO THE SCIENTIFIC ARTICLE IN ONLINE VERSIONS OF YOUR REPORT: http://www.nature.com/nbt/journal/v31/n4/full/nbt.2522.html

Prof. Dr. Dag Harmsen
Medical Faculty
University of Münster, Germany
Mobile: +49 (171) 2849378