PacBio Releases New Software Upgrade and Promises Better De Novo Assembly

PacBio Software Upgrade Promises Better De Novo Assembly

PacBio Software Upgrade Promises Better De Novo Assembly

Pacific Bioscices (PacBio) announced today that it is releasing a new software upgrade that will enhance De Novo genome assembly.  PacBio customers can download the software upgrade SMRT Analysis 1.4 on this Thursday 31st January.

The major highlight of the software upgrade is a new hierarchical de novo genome assembly process (HGAP) that can assemble the whole microbial and fungal genomes with PacBio long reads alone. PacBio says that this allow users to get better genome assemblies with a single library preparation and fewer SMRT Cells than “previous approaches that also required short-read sequencing technologies or circular consensus sequences”.

In addition to the new assembly algorithm, SMRT Analysis 1.4 has  a new multi-read consensus algorithm called Quiver to determine the finished genome sequence with great accuracy.  PacBio says that “Quiver can provide greater than 99.999% consensus accuracy for both resequencing and de novo assembly applications.”

PacBio could rope in the sequencing pioneer J. Craig Venter to vouch for the performance of PacBio RS and the new software upgrade. In the press release announcing the availability of PacBio software upgrade, J. Craig Venter said

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.

The new software upgrade also support full-length cDNA transcript analysis for understanding transcription, gene structure and alternative splicing. PacBio claims that the long PacBio reads from SMRT Sequencing technology “can span entire cDNA transcripts with a single read, revealing the complete exonic structure of transcripts.”

The new SMRT Analysis 1.4 upgrade also includes:

  • 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.

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