Debating PacBio: the #SMRTseq -Naomi Attar on July 23, 2013 at 2:59 pm
Debating PacBio: the #SMRTseq Tweet chat
Naomi Attar on July 23, 2013 at 2:59 pm In a recent Correspondence article published in Genome Biology, Rich Roberts, Mike Schatz and Mauricio Carneiro extolled the virtues of Pacific Biosciences’ SMRT sequencing platform. The article sought to address an impression held by many in the field that single-molecule sequencing is not yet a viable option, a view Roberts et al. believe to be wide of the mark. In particular, the long reads and non-biased error patterns produced by SMRT sequencing are praised as useful for a range of genomics applications, alongside the unique feature of direct base-modification readout.
We thought a discussion on the merits of SMRT sequencing and what its long term prospects may be would be timely and of interest to our Twitter audience, and so Genome Biology, together with Beyond The Genome, has decided to hold a Tweet chat.
Some points to consider
Availability: the number of PacBio machines in circulation is currently pretty limited – is there a need for more PacBio services to be provided by those institutes with machines to those without?
Cost: the initial outlay with PacBio is high if you are only going to use it for limited purposes, even though base-for-base it is competitively priced – its limitations mean that many users will use PacBio together with Illumina and so will have to shell out for two platforms. (A hybrid approach shows how SMRT and Illumina reads can complement each other very well).
Improving technology: SMRT sequencing is much improved since its early days and can now be used for many applications, as documented on PacBio’s blog. See, for example, this talk by Eric Schadt on sequencing whole human genomes.
Competitors: two competitors to think about might be Illumina’s Moleculo, which is now on the market, and Oxford Nanopore Technologies’s MinION and GridION, which aren’t.