Tuesday, August 19, 2014

Videos and Slides: Next-Generation Sequencing Technologies - Elaine Mardis (2014)

Last time I mentioned Elaine Mardis videos giving a summary of next generation sequencing the video shot up and garnered more than 127,893 viewers. Coincidence ? I think not :-)

Here is the new survey on Next Generation Sequencing where she talks about the current PacBio and Nanopore technology add-ons to the lab. I note the biology people liking the term "massively parallel" sequencing. Anyway, those third generation technologies are very interesting because instead of cutting DNA strands in small pieces and trying to put them back together, they output very long reads (up 50Kbp from 200bp for earlier next generation sequencing technology) thereby reducing much of the guessing in the read alignments. The current downside of those technologies are that they have large error rates. PacBio, for instance, with its SMRT technology has about 15pct error rate for a single strand of DNA but that error goes away when combining several DNA strand reading together down to 0.01pct overall. Nanopore, according to Elaine, is in the 30pct realm but one would have to check people looking into it to be really more accurate on that figure. Irrespective, the longer reads with oversampling means that one can get much nicer view of the genome that was, for chemical reasons, not reachable otherwise. I also note that the PacBio approach uses fluorescence and hence uses camera technology, one of the steamrollers. Fluorescence is not unheard of in compressive sensing and maybe an improvement of the technique might provide enhanced accuracy. The question is how do algorithms featured here on Nuit Blanche can help in realizing A Second Inflection Point in Genome Sequencing. (For people confused Next Generation sequencing refers to 2nd generation sequencing while third generation sequencing refers to newer sensors). More on that later.

Without further ado, here is a summary of sequencing technology as July 30th, 2014.

The slides are in Color or Grayscale

This lecture was part of a larger series of talks in Current Topics in Genome Analysis 2014

Also of interest: PBSuite, Software for Long-Read Sequencing Data from PacBio

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