X

Quality Statement

Pacific Biosciences is committed to providing high-quality products that meet customer expectations and comply with regulations. We will achieve these goals by adhering to and maintaining an effective quality-management system designed to ensure product quality, performance, and safety.

X

Image Use Agreement

By downloading, copying, or making any use of the images located on this website (“Site”) you acknowledge that you have read and understand, and agree to, the terms of this Image Usage Agreement, as well as the terms provided on the Legal Notices webpage, which together govern your use of the images as provided below. If you do not agree to such terms, do not download, copy or use the images in any way, unless you have written permission signed by an authorized Pacific Biosciences representative.

Subject to the terms of this Agreement and the terms provided on the Legal Notices webpage (to the extent they do not conflict with the terms of this Agreement), you may use the images on the Site solely for (a) editorial use by press and/or industry analysts, (b) in connection with a normal, peer-reviewed, scientific publication, book or presentation, or the like. You may not alter or modify any image, in whole or in part, for any reason. You may not use any image in a manner that misrepresents the associated Pacific Biosciences product, service or technology or any associated characteristics, data, or properties thereof. You also may not use any image in a manner that denotes some representation or warranty (express, implied or statutory) from Pacific Biosciences of the product, service or technology. The rights granted by this Agreement are personal to you and are not transferable by you to another party.

You, and not Pacific Biosciences, are responsible for your use of the images. You acknowledge and agree that any misuse of the images or breach of this Agreement will cause Pacific Biosciences irreparable harm. Pacific Biosciences is either an owner or licensee of the image, and not an agent for the owner. You agree to give Pacific Biosciences a credit line as follows: "Courtesy of Pacific Biosciences of California, Inc., Menlo Park, CA, USA" and also include any other credits or acknowledgments noted by Pacific Biosciences. You must include any copyright notice originally included with the images on all copies.

IMAGES ARE PROVIDED BY Pacific Biosciences ON AN "AS-IS" BASIS. Pacific Biosciences DISCLAIMS ALL REPRESENTATIONS AND WARRANTIES, EXPRESS, IMPLIED OR STATUTORY, INCLUDING, BUT NOT LIMITED TO, NON-INFRINGEMENT, OWNERSHIP, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. IN NO EVENT SHALL Pacific Biosciences BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, PUNITIVE, OR CONSEQUENTIAL DAMAGES OF ANY KIND WHATSOEVER WITH RESPECT TO THE IMAGES.

You agree that Pacific Biosciences may terminate your access to and use of the images located on the PacificBiosciences.com website at any time and without prior notice, if it considers you to have violated any of the terms of this Image Use Agreement. You agree to indemnify, defend and hold harmless Pacific Biosciences, its officers, directors, employees, agents, licensors, suppliers and any third party information providers to the Site from and against all losses, expenses, damages and costs, including reasonable attorneys' fees, resulting from any violation by you of the terms of this Image Use Agreement or Pacific Biosciences' termination of your access to or use of the Site. Termination will not affect Pacific Biosciences' rights or your obligations which accrued before the termination.

I have read and understand, and agree to, the Image Usage Agreement.

I disagree and would like to return to the Pacific Biosciences home page.

Pacific Biosciences
Contact:

Genome Biology Paper Highlights Affordability and Scale of PacBio-Based Finished Microbial Genomes

Monday, September 16, 2013

A new paper released in Genome Biology on September 13 from lead author Sergey Koren at the National Biodefense Analysis and Countermeasures Center offers a thorough overview of SMRT® Sequencing for microbes, from per-genome cost to potential for assembling complete genomes.

In “Reducing assembly complexity of microbial genomes with single-molecule sequencing,” Koren and co-authors consider microbial genome assembly, which evolved over time from the Sanger days of manually finished genomes to short-read sequencers that offered lots of sequence data but virtually no finished genomes. Today, that evolution has continued with SMRT® Sequencing, which allows for rapid and complete genome assembly. Less than a third of genomes in the Genomes OnLine Database are closed, according to the authors, and fewer still were considered fully finished. “This has hampered large-scale, structural analyses of bacterial genomes, and focused research instead on isolated genes and single-nucleotide polymorphisms,” Koren et al. write. Without knowledge of the full genome, microbiologists have been missing key information about pathogenicity, function, evolution, and more.

Single-molecule sequencing, on the other hand, provides a straightforward path to finished genomes, offering scientists the possibility for comparative genomic studies of many organisms, according to the paper. Indeed, based on an analysis of the repeat complexity of nearly 2,300 microbes, Koren et al. estimate that automated pipelines utilizing SMRT Sequencing “could automatically close >70% of the complete bacteria and archaea in GenBank, without the need for pair libraries….” To see how this would affect your favorite organism, check out paper co-author Adam Phillippy’s useful gap-prediction tool. Note: These results were based on a previous chemistry – using PacBio’s current chemistry with longer read lengths, the closure rate would be even higher.

The authors also looked closely at cost implications of finishing microbial genomes in this manner. Relying on a single, PacBio-only library preparation (instead of two or more preps required for hybrid assemblies) keeps costs down and accuracy up; “single-library assemblies are also more accurate than typical short-read assemblies and hybrid assemblies of short and long reads,” Koren et al. write. They note that closing more than 70% of known microbial genomes could be accomplished for about $900 per genome — or two SMRT Cells per organism using the PacBio RS II.

As part of this project, the scientists sequenced six genomes with varying GC content and complexity using Illumina®, 454®, and PacBio sequencers. For nearly all of the genomes, the PacBio-only assemblies “outperformed the hybrid assemblies both in terms of continuity, error rate, and the assembly likelihood score,” the authors write. “The assemblies presented here have good likelihood and finished-grade consensus accuracy exceeding 99.9999%.”

Koren and his collaborators note that with an affordable, high-quality approach to fully sequencing and finishing microbial genomes, there is now opportunity to “increase the number of completed genomes, improve the quality of microbial genome databases, and enable high-fidelity, population-scale studies of pangenomes and chromosomal organization.”

Subscribe for blog updates:

Archives