Comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

The Wellcome Trust Sanger Institute, UK,  recently published a comparison of the Ion Torrent PGM, Illumina Miseq, and Pacific Biosciences PacBio RS.  They compared the results obtained with those platforms to the performance of the Illumina HiSeq, the current market leader. In order to compare these platforms and get sufficient coverage depth to allow meaningful analysis, they sequenced a set of 4 microbial genomes with mean GC content ranging from 19.3 to 67.7%. Together, these represent a comprehensive range of genome content. They report their analysis of that sequence data in terms of coverage distribution, bias, GC distribution, variant detection and accuracy.

Sequence generated by Ion Torrent, MiSeq and Pacific Biosciences technologies displays near perfect coverage behaviour on GC-neutral and AT-rich genomes, but a profound bias was observed upon sequencing the extremely AT-rich genome of Plasmodium falciparum on the PGM resulting in no coverage for approximately 30% of the genome. We analysed the ability to call variants from each platform and found that we could call slightly more variants from Ion Torrent data compared to MiSeq data, but at the expense of a higher false positive rate. Variant calling from Pacific Biosciences data was possible but higher coverage depth was required. Context specific errors were observed in both PGM and MiSeq data but not in that from the Pacific Biosciences platform.

All three fast turnaround sequencers evaluated here were able to generate usable sequence. However there are key differences between the quality of that data and the applications it will support.


Quail M, Smith ME, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y. A tale of three next generation sequencing platforms:comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers. BMC Genomics. 2012 Jul 24;13(1):341. [Epub ahead of print] PubMed PMID: 22827831.

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