December 19, 2013 at 11:47 am
#UCDAssemble Workshop Covering Genome Assembly ...
PacBio Makes a Big Stir !!! Readers interested in sequence assembly may take a look at the tweets under hashtag #UCDAssemble. It is attended by a number of researchers, who are working on writing genome assembly programs or are heavy users of such programs (e.g. Jared Simpson, Jason Chin, Titus Brown, Lex Nederbragt, Nick Loman). The workshop is technically-oriented with a number of hands on exercises. We will summarize the key points for those without twitter access.
Conference-related documents are available here.(go to IHUB for link)
By Aaron Krol
Awarded in September of this year, the grant will culminate in a 300-person trial of the fine-tuned test before UC Davis prepares it for clinical release. PacBio is closely involved in the project, which could establish a unique position for the company in clinical use at a time when the sequencing industry is scrambling to enter the clinical market. Illumina, the world’s largest sequencing company, recently received FDA approval for a cystic fibrosis diagnostic, a landmark in medical genetics. QIAGEN, a multibillion-dollar diagnostics company, is preparing to release the new GeneReader instrument specifically for clinical use.
PacBio is smaller than either of these companies, but its SMRT sequencers are the only instruments that can access fragile X mutations. “We are right now in the business of facilitating sequencing that can’t be done using other techniques,” Turner, who is also principal investigator for the NIH grant, told Bio-IT World. “The longest read length of any technology other than PacBio is about one thousand bases, so they’re far short of being able to cover [the range of FMR1 mutations].”
Two aspects of SMRT technology – the acronym stands for single molecule, real time – give PacBio the coverage needed to delve into the black boxes of the genome. The first is a DNA polymerase engineered from the f29 bacteriophage. Bacteriophages, viruses that invade bacteria and replicate inside their hosts, use polymerases to copy their genetic sequences. The f29 phage is remarkable for replicating its entire, nearly 20,000-base genome in a single step, using just one enzyme. Armed with this highly accurate, long-reading polymerase, a SMRT sequencer can chew through thousands of bases using just one enzyme and one molecule of sample DNA. (Go to IHUB for full story & link)
PacBio, the UK’s Sanger Institute and Public Health England will analyse the genomes of 3,000 bacterial pathogens.
( "PacBio’s 3rd generation SMRT sequencing technology achieves the longest read lengths and highest consensus accuracy in the industry. Because the technology can directly detect base modifications, the epigenomes for bacteria can also be obtained with no additional data acquisition, providing unprecedented insight into the role of DNA methylation in bacterial pathogenicity.")!! (IHUB for full story)
Separately, analysts at Maxim Group raised their price target on shares of Pacific Biosciences of California from $4.00 to $8.00 in a research note to investors on Thursday, September 26th. They now have a “buy” rating on the stock.
(same link as last).
(Posted by Joseph Griffin on Dec 13th, 2013 Pacific Biosciences of California (NASDAQ:PACB) CEO Michael Hunkapiller purchased 100,000 shares of Pacific Biosciences of California stock on the open market in a transaction dated Thursday, December 12th. The shares were purchased at an average cost of $4.13 per share, with a total value of $413,000.00. Following the acquisition, the chief executive officer now directly owns 1,800,000 shares in the company, valued at approximately $7,434,000. The transaction was disclosed in a legal filing with the Securities & Exchange Commission, which is available at this link. on IHUB.
( This is being disscussed today) RNA-Seq @Illumina researchers may be interested in @Pacbio sequencing of Human MCF-7 Transcriptome.
(See todays PacBio Blog )
Wednesday, December 11, 2013
Embed Tweet Report Tweet 1 Favorite 10:53 AM - 11 Dec 13 · Details
(3 of 3) Convey’s groundbreaking hybrid-core computing architecture tightly integrates advanced computer architecture and compiler technology with commercial, off-the-shelf hardware—namely Intel® Xeon® processors and Xilinx® Field Programmable Gate Arrays (FPGAs). Particular algorithms are optimized and translated into code that’s loaded onto the FPGAs at runtime to accelerate applications that use these algorithms. The systems help customers dramatically increase performance over industry standard servers while reducing energy costs associated with high-performance computing.
“Adding PacBioToCA to the Convey Bioinformatics Suite reflects our ongoing commitment to the bioinformatics and life sciences community,” concluded Vacek. “We enjoy working with innovators to bring solutions to the industry that will help solve the challenges of the rapidly changing area of sequencing. We look forward to continuing to collaborate with Pacific Biosciences and others on optimization of bioinformatics workflows.”
Convey’s expanding bioinformatics suite is made up of a number of personalities including the Convey GraphConstructor™ for de novo short read assembly, Smith-Waterman for local sequence alignment, and Burrows-Wheeler Aligner for fast reference mapping.
About Convey Computer Corporation
Based in Richardson, Texas, Convey Computer breaks power, performance and programmability barriers with the world’s first hybrid-core computer—a system that marries the low cost and simple programming model of a commodity system with the performance of a customized hardware architecture. Using the Convey hybrid-core systems, customers worldwide in industries such as life sciences, research, big data, and the government/military enjoy order of magnitude performance increases while reducing acquisition and operating costs.
(for link go IHUB to )
(2 of 3)Last year, Dr. Sergey Koren, Bioinformatics Scientist at the National Biodefense Analysis and Countermeasures Center, and his colleagues developed an assembly strategy that uses short sequences (either from PacBio circular consensus sequencing or short read technologies) typical of high-throughput sequencers to correct the errors in PacBio reads. This strategy was subsequently extended to use shorter single-molecule reads to correct the longest ones. These techniques deliver high-accuracy long reads, resulting in gold standard genome assemblies.
For larger genomes, the PacBioToCA algorithm can be time-consuming; therefore, Koren collaborated with Convey to optimize the PacBioToCA algorithm for Convey’s highly parallel HC systems. The optimized version of PacBioToCA runs much faster on the Convey HC servers because the alignment algorithm it uses is significantly faster on a Convey HC-2ex server than the best implementation on a standard server.
“It has been shown that long PacBio reads processed with PacBioToCA lead to such high-quality assemblies, researchers are saved the significant subsequent cost of manual finishing,” explained Kevin Corcoran, Senior Vice President of Market Development at Pacific Biosciences. “The combination of the PacBioToCA algorithm and a Convey HC system allows our customers to dramatically speed up research for projects in areas such as functional genomics, comparative genomics, and beyond.”
Wednesday, December 11, 2013
PacBioToCA Is the Newest Addition to Convey’s Expanding Bioinformatics Suite, Helping to Speed Genomic Research
Richardson, TX (PRWEB) December 11, 2013
Convey Computer™ Corporation announced today the newest addition to Convey’s expanding bioinformatics suite, PacBioToCA, an application that facilitates the assembly of genomes sequenced with Pacific Biosciences® long-read technology. Optimized to take advantage of the highly parallel processing architecture of the Convey hybrid-core (HC) server, PacBioToCA delivers six to fifteen times acceleration.
Researchers running PacBioToCA on Convey HC systems for sequencing and assembly are seeing exceptional results. “The speed up is significant; but even more importantly, researchers are now able to test more parameters,” commented Dr. George Vacek, Director of Convey Computer’s Life Sciences business unit. “Achieving results in a matter of days instead of weeks allows them to refine their approach and get better answers.”
The PacBio® RS II DNA Sequencing System, from Pacific Biosciences (NASDAQ: PACB), helps scientists solve genetically complex problems. Their single-molecule sequencing instruments can generate industry-leading sequence read lengths that dramatically improve genome and transcriptome assembly.
Researchers are attracted to the exceptionally long PacBio reads because they can deliver higher quality assemblies. Prior to the development of algorithms optimized for PacBio read data (such as PacBioToCA), single-pass error rates had been perceived to limit their utility in de novo assembly. (pot 1 of 2)
Oxford Nanopore has raised £40 million in new funding through a private placement of ordinary shares, bringing the total amount raised to £145 million since the foundation of the Company in 2005 !!!( Thats almost 1/4 of a BILLION $$$$) Yet to produce NOTHING but BS in 8 YEARS!!!
This study reports the use of single molecule consensus sequencing using the Pacific Biosciences RS for microsatellite discovery. The advantage over other next-generation sequencing systems is the random error model and the capability for sequencing the same library molecule several times, thereby generating high quality consensus sequences. The relatively long library molecules in combination with high consensus accuracy are excellent templates for primer design as the reads cover larger flanking regions of the identified microsatellites compared to Illumina, 454 or Ion Torrent sequencing reads. !!!
The genomic shotgun approach for microsatellite discovery using the PacBio PacBio real-time sequencing system, which is based on the CCS approach. CCS therefore represents a combination of unbiased random shotgun sequencing with high consensus coverage of the template molecule. We have therefore explored the usability of CCS reads for microsatellite discovery and subsequent primer design.
A single sequencing run costing ~$600 (including library preparation) should therefore generate a minimum of 30,000 CCS reads, a 20-fold increase compared with our study, yielding ~6500 potential loci even in microsatellite poor bird genomes. Several price calculations for different PacBio sequencing chemistry combinations can be found in the recent study by Koren et al. (18). This puts the cost of microsatellite discovery using PacBio sequencing between that of 454 and Illumina sequencing (4). Our approach provides a useful alternative when cost reduction using multiplexing is not practicable, and microsatellite array length is to be determined directly from the data for prioritized locus testing.(More on IHUB for lik)
Submitted by jabylyn 29 minutes ago - PacBio sequencing of gene families — A case study with wheat gluten genes
mainly accumulate in storage proteins called gliadins and glutenins. Gliadins contain a/ß-, ?- and ?-types whereas glutenins contain HMW- and LMW-types. Known gliadin and glutenin sequences were largely determined through cloning and sequencing by capillary electrophoresis. This time-consuming process prevents us to intensively study the variation of each orthologous gene copy among cultivars. The throughput and sequencing length of Pacific Bioscience RS (PacBio) single molecule sequencing platform make it feasible to construct contiguous and non-chimeric RNA sequences. We assembled 424 wheat storage protein transcripts from ten wheat cultivars by using just one single-molecule-real-time cell. The protein genes from wheat cultivar Chinese Spring are comparable to known sequences from NCBI. We demonstrated real-time sequencing of gene families with high-throughput and low-cost. This method can be applied to studies of gene amplification and copy number variation among species and cultivars.
( IHUB for link)
More from User Group Meeting
Alex Copeland, DOE – Joint Genome Institute
Copeland offered an overview of the institute’s microbial and fungal reference assembly pipeline, describing their experience with a 10x increase in read length and total throughput in three years on the PacBio platform. He shared that the team has shifted to a PacBio-only pipeline, and that they are finishing genomes on the platform for less than $2,000.
Lance Hepler, Center for AIDS Research, UC San Diego
Hepler used the PacBio RS to study intra-host diversity in HIV-1. He compared PacBio’s performance to that of 454®, the platform he and his team previously used. Hepler noted that in general, there was strong agreement between the platforms; where results differed, he said that PacBio data had significantly better reproducibility and accuracy.
John Huddleston, University of Washington
Huddleston is looking at challenging regions in the human genome, noting
that assembly accuracy needs to be quite high to resolve breakpoints and
reconstruct duplication architectures. His team is working with BACs to
validate the use of the PacBio platform as a faster, more cost-effective
alternative to Sanger. In one study, his team found that PacBio results
had 99.994% identity with Sanger results and showed uniform coverage
across the clone.
Lisbeth Guethlein, Stanford University School of Medicine
Guethlein looked at highly repetitive and variable regions of the
orangutan genome. Guethlein reported that “PacBio managed to accomplish
in a week what I have been working on for a couple years,” (with
Sanger) and the results were concordant.
(LOT More,go to IHUB for link)
Mick Watson - 23 Oct. "There it is RT @EpgntxEinstein: Roche to develop a smaller (cheaper) PacBio machine focused on clinical sequencing" ?? (Mick Watson is Genomicist / Bioinformatician, Director of ARK-Genomics, a high-throughput facility at The Roslin Institute).
Post #2-Lance Hepler from UC San Diego’s Center for AIDS Research used the PacBio RS to study intra-host diversity in HIV-1. He compared PacBio’s performance to that of 454® sequencer, the platform he and his team previously used. Hepler noted that in general, there was strong agreement between the platforms; where results differed, he said that PacBio data had significantly better reproducibility and accuracy. “PacBio does not suffer from local coverage loss post-processing, whereas 454 has homopolymer problems,” he noted. Hepler said they are moving away from using 454 in favor of the PacBio system. WOW !!!!
We were delighted to have two speakers from the Joint Genome Institute, which has become a power user of the PacBio technology. Alex Copeland offered an overview of the institute’s microbial and fungal reference assembly pipeline, where de novo genome sequencing is especially important. He described their experience with a 10x increase in read length and total throughput in three years on the PacBio platform. He also discussed the evolution of their pipeline from Sanger sequencing to the Illumina® and PacBio platforms, going from a median of 49 contigs per microbial genome with Sanger, to 69 with Illumina sequencing, and to 10 or fewer with the PacBio system. Copeland noted that after producing 100x coverage of long reads (10 kb inserts), PacBio users can reliably assemble a genome into 10 contigs or fewer. He said that the team has shifted to a PacBio-only pipeline, and that they are finishing genomes on the platform for less than $2,000. ( for link,go to PACB BLOGS)
on the HGAP and (Illumina) Celera pipelines, he
adds, “we’re developing our own postprocessing
steps to make even further
improvements to genome assembly.
For other teams considering whether
SMRT Sequencing is the right choice
for them, Tallon says: “If you’re going
to be working with small genomes,
value complete or nearly finished
genome sequences, and are looking at
base modifications in addition to the
genome sequence, there’s no better
platform out there.”
without manual finishing efforts,” Tallon says. With SMRT Sequencing, his team is consistently finishing genomes. “Our biggest challenge is getting sufficient high-quality DNA to start a project. If we get that, the genomes are going to close more often than not.”
For more on the GRC’s use of the PacBio system, including details on how the lab optimized its SMRT pipeline, read the complete profile. You can also visit the GRC blog or attend their upcoming applications seminar to hear how the PacBio RS II can advance your research on Thursday, November 7 at 11:00 AM. (for the whole story and link,go to IHUB MB)
Posted on October 29, 2013 by nsengamalay Join us for an IGS-sponsored PacBio seminar Thursday, 11/7 at 11:00 in Discovery Auditorium, Biopark II. Come see how SMRT sequencing can advance your research!