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. Everyone is welcome to participate in the Tweet chat – all you have to do is include #SMRTseq in your tweets at the designated time.
It’s an interesting time for SMRT sequencing – squeezed between the ubiquity of short read sequencing at the present time and the promise of much-hyped long read options, such as Moleculo and nanopore sequencing, in the future (with the former now having entered the market), it is competing on two fronts. And yet it is also emerging from a time when it was universally dismissed as unreliable into a ‘publication competent’ phase, with appearances in an increasing number of scientific papers and presentations.
The Tweet chat panel
Two authors of the Correspondence article, Mike Schatz and Mauricio Carneiro, have kindly agreed to particpate in the Tweet chat. Other panelists include Mario Caccamo (Mike Schatz’s colleague on the Beyond The Genome organizing committee), Jason Merkin (Burge lab) and Eric Johnson (SNPsaurus). Anyone with a Twitter account and an interest in PacBio sequencing is encouraged to join the panelists in discussing our Tweet chat questions.
Where and when?
The Tweet chat will take place July 31 at 11 am EST/4 pm BST for a one hour duration. We will use the hashtag #SMRTseq to identify tweets.
Over the course of the hour, we will ask the following questions:
Icebreaker: Introductions – if you are a PacBio user, how did you start using it and what was your initial impression?
1/ Why do you think uptake of PacBio has not been greater? What would have to change in order to increase uptake of PacBio?
2/ Related to 1/, of all the different benefits of SMRT sequencing, which do you think will be the most persuasive in encouraging people to adopt it?
3/ Its utility for small genome completion is probably not debated, but how much scope is there for using PacBio to study more complex genomes?
4/ What are the key considerations to weigh up when considering whether PacBio is the best option for a project?
5/ What developments in the dynamics of the sequencing market do you foresee impacting upon PacBio’s popularity?
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.