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David or Goliath: the first SMRT bench-top sequencer

APRIL FOOLS!

New sequencing reagents to scale (courtesy of PowerPoint)
New sequencing reagents to scale (courtesy of PowerPoint)

Word through the grapevine is that PacBio are probably going to announce their latest sequencer today, as part of their on going collaboration with Roche. So what do we know? Firstly, the size of the sequencer has been greatly reduced from the behemoth that is the PacBio RS II to what is reportedly a mere H135 x W240 x D85mm, making it one of the smallest NGS platforms to date. It also looks like size is not directly proportional to the expected read length, as the new system is rumored to offer reads of up to 100 kb, moving it into the size range of genome mappers like the Opgen Argus and Bionano Irys. But what has shrunk by several factors is the reagents, with SMRT cells now being significantly more compact – removing all the additional plastic while keeping the same size ZMW array we’re used to. In addition:

  • New DNA/Polymerase Binding Kit P0 for longer reads.
  • External transmitter for cloud computing and data storage in the field.
  • Carry handle to offer researchers the same portability as Oxford Nanopore’s minION.

But have they fixed the read quality?

No, but the read length is still increasing and this could be even more exciting. Who needs Q30 when you have reads approaching 100 kb? What’s more, as alluded to in a interview with Ken Dewar from McGill University last year, you’re going to have so many base calls that you won’t know what to do with them all. But, Pacbio has listened and are planning to update their SMRT Analysis Software to put all those additional base calls (longer than the incorporation) to good use. See the interview with Ken Dewar here for a taste of things to come.

Where PacBios are born (actually from the Pacbio media kit, pretty cool)

Will the Pacbio RS II become an obsolete monolith? 

While the new Pacbio system is expected to perform as well or better than previous iterations, miniaturization of the technology mean it should be possible to use all the additional space inside. This could mean the ability to run more samples at once allowing higher throughput SMRT sequencing or maybe a good spot to hide from your PI when a single sequencing run doesn’t produce the single contig assembly that was expected.

Published inGenomics

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