Ion Torrent PGM, Miseq, PacBio RS Comparison

Ion Torrent PGM, Miseq, PacBio RS Comparison
Justin Johnson from EdgeBio summarises the work done by Wellcome Trust Sanger Institute
We wanted to highlight and summarize one such comparison that we found particularly informative.  The Wellcome Trust Sanger Institute recently published a platform comparison of the Ion Torrent PGM, Illumina Miseq, and Pacific Biosciences PacBio RS.  For the comparison, four microbial genomes were sequenced with a GC content ranging from 19 percent to 68 percent.  Datasets generated from each platform were down sampled to represent an average coverage of 15X and were aligned to the 4 microbial reference sequences.  For analysis they used a SAMtools pipeline for Illumina, SAMtools and the Ion Torrent variant calling pipeline for the PGM and the SMRT portal pipeline for PacBio.  To examine SNP calling accuracy, the researchers aligned the datasets from Staphylococcus aureus to a closely related strain and then compared the SNP calls to those found after aligning the S. aureus genome to the related strain.  These platforms were compared in terms of 

1. genome coverage,
2.  GC-Bias, 
3. error rate,
4.  SNP calling,
5.  and cost. (Miseq cheapest /gigabase if you ignore GAIIx & HiSeq2000 )

Caveats: 

Sejal Sheth, VP of strategic marketing for PacBio said that this study looked at standard metrics used to evaluate short-read technologies “which are not necessarily as relevant for long read technologies”.  After noting that the release of new chemistry and algorithms address some of the issues found in the study, Sheth stated that “for the purposes of comparing platforms, it is consensus accuracy, not raw read accuracy that is the relevant metric”.  Consensus accuracy was not addressed in this study.