This class has been running since 2010-11, on the following principle:
¦autumn semester: isolate bacterial DNA, sequence using Illumina, assemble;
¦spring semester: close assembly gaps, annotate genome.
As anyone following genomics knows, the times they are a’changing again and again, so this is less and less state-of-the-art. So we have decided to try a new course plan this year, taking advantage of the progress in bacterial genome sequencing with long PacBio reads.
Our new principle is, hopefully:
¦autumn semester: isolate bacterial DNA, sequence using PacBio, assembly trivial, annotate genome;
¦spring semester: RNA-seq under 2 growth conditions, experiments, Illumina sequencing and bioinformatics analysis.
“Hopefully” because PacBio on bacteria is not yet routine, depending on the genus and the growth conditions. We are thus trying two different bacteria, a Pseudomonas which has a cool story for the RNA-seq part, and a Caulobacter which has been shown to work with PacBio. Preliminary studies on the Pseudomonas are somewhat discouraging for the PacBio sequencing, but we will still try, with adaptations of the protocol. We will also keep the possibility to reverting to Illumina sequencing plus assembly, but we would like to avoid that (if Caulobacter is plan B, this is plan C).
And of course, we have never done RNA-seq with master students, so this year will be a new adventure, comparable to our first course in 2010. Stressful and exciting.
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? Our first student genome paper is out: Miyazaki et al Environ MicrobiolOne Response to A new adventure: PacBio sequencing and RNA-seq in the classroom
Winship Herr says:
September 18, 2014 at 14:31
This is a super cool course. My first Master First-step project was to sequence 100 nucleotides of the lac operon
Illumina has moleculo technology which is based on shearing DNA and then assembling individual segments. I don't think it even come close to PacBio technology. I think PacBio has huge potential if they can release smaller and cheaper sequencer. In clinical and personalized genome sequencing PacBio will provide best assembly without doubt, and that's why it'll be winner in long term. In clinical and personalized genome space you want most accurate assembly and PacBio has that...
With Illumina, the dominant player in the NGS market, claiming this year that they’ve reached that target with their HiSeq X Ten system, it’s fair to stop and ask just what has been achieved. What do you get for that $1,000? And furthermore, where does NGS go from here?
Beginning next week, we're launching a new series, The Rise of Long Read Sequencing.
I first heard “long read” sequencing differentiated from “short read” in an interview with Mike Hunkapiller, CEO of Pacific Biosciences last year. I had asked him the obvious question about how he expects to compete with Illumina, and he responded saying that “short read technologies” had serious draw backs.
“Wait a minute,” I remember thinking at the time, “did Mike just dismiss Illumina’s technology out right? And what are these long reads he’s talking about.”
(Very interesting article)!! For link,Go to IHUB PACB M.B.
I want to see smaller and cheaper sequencer from PacBio, expensive sequencer is a huge barrier. If they release a smaller and cheaper sequencer then that they can gain lot of Roche 454, IonTorrent and MiSeq business.
Last quarter down to 5. If the number climbs back to 7, then PPS will keep going up. If it stays around 5 or even less. PPS will drop hugely. There is nothing simpler than this stock.
Luckily, I sold part of my position yesterday at 6, and bot it back today at 5.24.
Sometimes, the reason is the HST guys, naked shorting a small cap with no real support. There is certainly no public news that would have sparked this selling.
If it goes back to 6, and it will, I make well over 10%. To me, the only question is when will that happen, maybe not this month, but in 60 days? I'll take 10+% in 60 days.
Like I said. This is the best of breed,and it's just now starting to get on many investors radar screens. Once we get a little more press time and the company starts it's investor confrences, then it should really start moving the needle just like Illumina did.
Sentiment: Strong Buy