January 29, 2013

Pacific Biosciences’ Software Upgrade Enhances De Novo Genome Assembly, Variant Calling and cDNA Transcript Analysis

MENLO PARK, Calif., Jan. 29, 2013 (GLOBE NEWSWIRE) — Pacific Biosciences of California, Inc. (Nasdaq:PACB) provider of the PacBio® RS High Resolution Genetic Analyzer, today announced it is releasing a new software upgrade that provides higher quality genome assemblies with near perfect base level accuracy in addition to other key features. The software upgrade extends the range of projects that uniquely benefit from the company’s Single Molecule, Real-Time (SMRT®) DNA Sequencing method, and will be available to customers for download on January 31st.

SMRT Analysis 1.4 includes a new hierarchical de novo genome assembly process (HGAP), which allows researchers to assemble entire microbial and fungal genomes solely using PacBio long reads. As a result, users can generate better assemblies with a single library preparation and fewer SMRT® Cells than previous approaches that also required short-read sequencing technologies or circular consensus sequencing.

SMRT Analysis 1.4 also incorporates a new multi-read consensus algorithm called Quiver to determine the finished genome sequence with exceptional accuracy. Quiver can provide greater than 99.999% consensus accuracy for both resequencing and de novo assembly applications.

“The extra-long sequence reads and the subsequent highly accurate de novo assemblies produced by the PacBio RS through the latest software enhancements have immensely improved our ability to discover and understand novel genomes cost-effectively,” said J. Craig Venter, Ph.D., Founder, Chairman, and Chief Executive Officer at The J. Craig Venter Institute and CEO of Synthetic Genomics.

The software upgrade also includes support for analyzing full-length cDNA transcripts, facilitating understanding of transcription, gene structure and alternative splicing. Unlike any other sequencing technology, SMRT Sequencing can span entire cDNA transcripts with a single read, revealing the complete exonic structure of transcripts.

Additional features of the new SMRT Analysis 1.4 upgrade include:

  • Support for analysis of barcoded samples;


  • Improvements to the tools for analyzing and visualizing bacterial methylomes, a capability unique to SMRT Sequencing;


  • Enhanced user and group permissions to help sequencing centers and core labs control what data is presented to end users.

“We are committed to continually improving the performance of the PacBio RS, in part through developing software enhancements designed to leverage the unique characteristics of our system,” said Kevin Corcoran, Senior Vice President of Market Development at Pacific Biosciences. “With long sequence reads, gold standard accuracy and higher quality assemblies, the genomics community can enjoy the benefits of truly finished genomes through SMRT Sequencing.”

The new SMRT Analysis software upgrade is available for download from Pacific Biosciences’ community website, along with sample data and protocols for cDNA sample preparation and barcoding. To access the software, data, and documentation, visit

For more information on the new SMRT Analysis software and the PacBio RS High Resolution Genetic Analyzer, please visit  

About Pacific Biosciences

Pacific Biosciences of California, Inc. (Nasdaq:PACB) offers the PacBio® RS High Resolution Genetic Analyzer to help scientists solve genetically complex problems.  Based on its novel Single Molecule, Real-Time (SMRT®) technology, the company’s products enable: targeted sequencing to more comprehensively characterize genetic variations; de novo genome assembly to more fully identify, annotate and decipher genomic structures; and DNA base modification identification to help characterize epigenetic regulation and DNA damage. By providing access to information that was previously inaccessible, Pacific Biosciences enables scientists to increase their understanding of biological systems.


         Maurissa Messier

         For Pacific Biosciences



         Trevin Rard

         Pacific Biosciences


Source: Pacific Biosciences of California, Inc.

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