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#SMRTSeq Tweet Chat: Users Weigh in on Current Applications and Future Outlook for PacBio Sequencing

Thursday, August 1, 2013

Today offered something new for the PacBio® team: our SMRT® technology was the subject of a tweet chat hosted by Genome Biology. For one hour, editors at the journal along with two authors of a recent commentary article on SMRT Sequencing and additional guest panelists participated in a live discussion on Twitter about the PacBio platform. Thanks to scientists Mike Schatz, Mauricio Carneiro, Mario Caccamo, Jason Merkin, and Eric Johnson, as well as Genome Biology editors Clare Garvey and Naomi Attar, for managing the chat. You can check it out here.

It was unclear how the Twitterati would manage a full technical discussion in 140-character increments — but somehow they managed to capture great intel about our long-read technology in a (somewhat limiting) short-read format! Participants who had generated or analyzed their own PacBio data had several common applications, including genome assembly, genotyping and variant validation, DNA modifications, and methylation studies.

In particular, people mentioned certain targeted uses that they said were difficult or impossible with other sequencers: getting through repeat regions, full-length isoform sequencing, and uncharacterized structural variation. They said that PacBio’s unique ability to provide epigenetic data and uniform coverage in extreme GC regions was quite useful. “I use PacBio because nothing else can handle trinucleotide repeats,” tweeted Erick Loomis (@ErickLoomis).

There was some discussion around bioinformatics, with users mentioning that algorithms are not as fully hammered out as those for second-gen sequencers, which have been around much longer; there is still a need for better software, they said.

We were especially glad to see broad consensus around the advantages of our new release, the PacBio RS II sequencer. The Institute for Genome Sciences at the University of Maryland tweeted that throughput had increased about three-fold with the upgrade. A run earlier this week yielded reads averaging 6,000 bases and more than 400 megabases per SMRT Cell, the institute said.

In a discussion about using SMRT Sequencing for more complex genomes, it was terrific to find that many users are already going beyond microbes. Participants mentioned using PacBio data for fish, fly, and even human genome analysis as examples of projects that have already been successfully completed.

We’re eager to keep the conversation going with anyone interested in learning more about the SMRT Sequencing platform and will continue to use #SMRTSeq in the future!

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