Comparing Next-Gen Sequence Data from Ion torrent, Pacific Biosciences and Illumina MiSeq Sequencers

Although there is no doubt, Illumina is the leader in the next-gen sequencing industry, the Next-gen sequencing space is buzzing with competitions. Each major player in the Next-gen sequencing industry is coming up updates that improve upon its previous version. The interesting and the hard to answer question what is the best sequencer for a given application?

A team of scientists from Sanger group, as come up with a new paper that compares the sequence data from on Torrent’s PGM, Pacific Biosciences’ RS and the Illumina MiSeq with the performance of the Illumina HiSeq.

The paper titled “A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers“, by Michael Quail, Miriam E Smith, Paul Coupland, Thomas D Otto, Simon R Harris, Thomas R Connor, Anna Bertoni, Harold P Swerdlow and Yong Gu on BMC Genomics July 2012.

Here is the abstract.

Background
Next generation sequencing (NGS) technology has revolutionized genomic and genetic research. The pace of change in this area is rapid with three major new sequencing platforms having been released in 2011: Ion Torrent’s PGM, Pacific Biosciences’ RS and the Illumina MiSeq. Here we compare 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, we have 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. Here we report our analysis of that sequence data in terms of coverage distribution, bias, GC distribution, variant detection and accuracy.

Results
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.

Conclusions
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