This Day On The Street
Continue to site
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

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

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

Check Out Our Best Services for Investors

Action Alerts PLUS

Portfolio Manager Jim Cramer and Director of Research Jack Mohr reveal their investment tactics while giving advanced notice before every trade.

Product Features:
  • $2.5+ million portfolio
  • Large-cap and dividend focus
  • Intraday trade alerts from Cramer
Quant Ratings

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
Stocks Under $10

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

Product Features:
  • Model portfolio
  • Stocks trading below $10
  • Intraday trade alerts
14-Days Free
Only $9.95
14-Days Free
Dividend Stock Advisor

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
  • Updates with exact steps to take - BUY, HOLD, SELL
Trifecta Stocks

Every recommendation goes through 3 layers of intense scrutiny—quantitative, fundamental and technical analysis—to maximize profit potential and minimize risk.

Product Features:
  • Model Portfolio
  • Intra Day Trade alerts
  • Access to Quant Ratings
Real Money

More than 30 investing pros with skin in the game give you actionable insight and investment ideas.

Product Features:
  • Access to Jim Cramer's daily blog
  • Intraday commentary and news
  • Real-time trading forums
Only $49.95
14-Days Free
14-Days Free


Chart of I:DJI
DOW 17,888.35 +168.43 0.95%
S&P 500 2,102.63 +22.22 1.07%
NASDAQ 5,156.3060 +47.64 0.93%

Free Reports

Top Rated Stocks Top Rated Funds Top Rated ETFs