This Day On The Street
Continue to site right-arrow
This account is pending registration confirmation. Please click on the link within the confirmation email previously sent you to complete registration.
Need a new registration confirmation email? Click here
Stocks Under $10 with 50-100% upside potential - 14 days FREE!

New Assembly Method Published For Rapid And Automated Genome Sequencing Using Long-Read, Single Molecule, Real-Time (SMRT(R)) Sequencing

Stocks in this article: PACB

MENLO PARK, Calif., May 6, 2013 (GLOBE NEWSWIRE) -- Researchers from Pacific Biosciences of California, Inc., (Nasdaq:PACB), the U.S. Joint Genome Institute and the University of Washington have published a new method for assembling high-quality genomes from Single Molecule, Real-Time (SMRT ®) DNA sequencing. Published in the May 5 edition of Nature Methods i, the paper by Chin et al. describes the hierarchical genome assembly process ( HGAP) and demonstrates the method for efficient, automated de novo assembly from genomic DNA to a finished genome sequence for several microorganisms and a human bacterial artificial chromosome (BAC) clone. As part of the paper, the authors also describe a new consensus algorithm, Quiver, that achieves highly accurate de novo genome sequence results exceeding 99.999% (QV 50) accuracy.

Finished genomes are crucial for understanding microbes and advancing the field of microbiology. ii Previous attempts for obtaining the complete genome sequence of microbes in an automated, high-throughput manner have challenged researchers. For example, with second-generation sequencing methods, short read lengths inhibit the ability to resolve long repeats, resulting in unfinished, fragmented draft assemblies. Further, extreme sequence contexts, such as GC- or AT-rich regions, or palindromic sequences, lead to gaps in draft genome assemblies that cannot be covered using these second-generation methods. As a result, Sanger sequencing has typically been employed for finishing microbial genomes, but due to its laborious and low-throughput nature this process is slow and expensive.

More recently, hybrid-assembly approaches have been described in which long PacBio reads were used in combination with short-read data iii,iv. Building on these advances, in this new paper the authors utilize just a single, long-insert shotgun DNA library in conjunction with SMRT Sequencing, thereby removing the need for additional sample preparation and sequencing data sets required for previously described hybrid strategies. A paper describing a similar strategy and assembly results by S. Koren, A. Phillippy, and colleagues from the National Biodefense Analysis and Countermeasures Center, Frederick, MD, and the United States Agriculture Department has been deposited in a pre-print archive.

"This approach can close the large gap that currently exists between 'draft' and high-quality 'finished' genomes," said Jonas Korlach, senior author on the paper and Chief Scientific Officer at Pacific Biosciences. "Further, the ability to automatically and cost-effectively assemble genomes independent of the availability of a reference sequence can be critical in the rapid characterization of new pathogen strains."

1 of 2

Select the service that is right for you!

Action Alerts PLUS
Try it NOW

Jim Cramer and Stephanie Link actively manage a real portfolio and reveal their money management tactics while giving advanced notice before every trade.

Product Features:
  • $2.5+ million portfolio
  • Large-cap and dividend focus
  • Intraday trade alerts from Cramer
  • Weekly roundups
TheStreet Quant Ratings
Try it NOW
Only $49.95/yr

Access the tool that DOMINATES the Russell 2000 and the S&P 500.

Product Features:
  • Buy, hold, or sell recommendations for over 4,300 stocks
  • Unlimited research reports on your favorite stocks
  • A custom stock screener
  • Upgrade/downgrade alerts
Stocks Under $10
Try it NOW

David Peltier, uncovers low dollar stocks with extraordinary upside potential that are flying under Wall Street's radar.

Product Features:
  • Model portfolio
  • Stocks trading below $10
  • Intraday trade alerts
  • Weekly roundups
Dividend Stock Advisor
Try it NOW

Jim Cramer's protege, David Peltier, identifies the best of breed dividend stocks that will pay a reliable AND significant income stream.

Product Features:
  • Diversified model portfolio of dividend stocks
  • Alerts when market news affect the portfolio
  • Bi-weekly updates with exact steps to take - BUY, HOLD, SELL
Real Money Pro
Try it NOW

All of Real Money, plus 15 more of Wall Street's sharpest minds delivering actionable trading ideas, a comprehensive look at the market, and fundamental and technical analysis.

Product Features:
  • Real Money + Doug Kass Plus 15 more Wall Street Pros
  • Intraday commentary & news
  • Ultra-actionable trading ideas
Options Profits
Try it NOW

Our options trading pros provide daily market commentary and over 100 monthly option trading ideas and strategies to help you become a well-seasoned trader.

Product Features:
  • 100+ monthly options trading ideas
  • Actionable options commentary & news
  • Real-time trading community
  • Options TV
To begin commenting right away, you can log in below using your Disqus, Facebook, Twitter, OpenID or Yahoo login credentials. Alternatively, you can post a comment as a "guest" just by entering an email address. Your use of the commenting tool is subject to multiple terms of service/use and privacy policies - see here for more details.
Submit an article to us!


DOW 17,804.80 +26.65 0.15%
S&P 500 2,070.65 +9.42 0.46%
NASDAQ 4,765.38 +16.9840 0.36%

Brokerage Partners

Rates from

  • Mortgage
  • Credit Cards
  • Auto

Free Newsletters from TheStreet

My Subscriptions:

After the Bell

Before the Bell

Booyah! Newsletter

Midday Bell

TheStreet Top 10 Stories

Winners & Losers

Register for Newsletters
Top Rated Stocks Top Rated Funds Top Rated ETFs