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
Rest of Article:
indicating that they have k-mers in common; close matches are overlapped to assemble the whole genome.
According to the authors, this process is so fast that an E. coli genome can be assembled de novo using MHAP in essentially the same amount of time it would take to create a reference-guided assembly of the same genome from short Illumina reads. This would put de novo assembly within reach for small labs that previously only had access to the computing resources for reference-guided assembly. MHAP sees even greater gains in efficiency with larger, eukaryotic genomes.
The authors used MHAP for assembly of a human genome, plus genomes of the bacterium E. coli, the yeast S. cerevisiae, the fruit fly D. melanogaster, and the plant A. thaliana. All these assemblies will be made freely available in GenBank. While none of the assemblies has yet been thoroughly vetted, the authors suggest that their assemblies may have closed gaps in the D. melanogaster, A. thaliana and even human reference genomes, thanks to their ability to use long-read sequencers. The most significant benefit of MHAP, however, is the time and cost savings to genomics labs. Both the D. melanogaster and A. thaliana genomes were assembled on a desktop computer in a matter of days; compared to an assembly of the fruit fly genome using the previous alignment tool BLASR, MHAP
By Bio-IT World Staff
August 15, 2014 | This Thursday, a team of bioinformaticians from the National Biodefense Analysis and Countermeasures Center, the University of Maryland College Park, and sequencing company Pacific Biosciences posted information on their tool MHAP to the life sciences preprint server bioRxiv. MHAP, or MinHash Alignment Process, is a dramatically faster method for ordering DNA fragments sequenced on long-read technologies like the PacBio RS II Sequencer or the Oxford Nanopore MinION, making it easier to assemble whole genomes from scratch without the use of a reference genome. Bio-IT World previously covered MHAP following a presentation by senior author Adam Phillippy at the PacBio User Group Meeting this June; however, the newly released paper features much greater detail, including assemblies of the human genome and four important model organisms.
As the price of DNA sequencing continues to fall, the barrier to analyzing genomes is increasingly the compute power needed to make sense of the raw sequencing data. This is especially true for de novo whole genome assembly, where software tools have typically fallen back on the brute force, computationally demanding method of comparing every DNA fragment's entire sequence against every other fragment in search of overlaps.
MHAP, created by Konstantin Berlin and Sergey Koren, instead renders each fragment as a short series of numbers generated through hash functions. Briefly, every DNA fragment fed into MHAP is split into a string of k-mers (the authors recommend 16-mers for a human genome). Each k-mer is then subjected to the same series of hash functions, which output short numbers. For each hash function, only the smallest of these numbers is stored to identify the DNA fragment. Thus, the fragment is reduced to one number for each hash function, and each of those numbers corresponds to a single k-mer. MHAP can then search for fragments with many of the same identifying numbers, indicating