Analyzing Single-Molecule, Real-Time DNA Sequencing Data with SMRT® Analysis

SMRT Analysis is a powerful, open-source bioinformatics software suite available for analysis of DNA sequencing data from Pacific Biosciences’ SMRT technology.  Users can choose from a variety of analysis protocols that utilize PacBio^® and third-party tools.  Analysis protocols include de novo genome assembly, cDNA mapping, DNA base-modification detection, and long-amplicon analysis to determine phased consensus sequences.  The browser-based SMRT Portal GUI offers push-button analysis, allowing the user to create, submit, and monitor analysis jobs.  The underlying algorithms can be accessed on the command-line for pipeline development with SMRT Pipe, utilizing LIMS-friendly APIs and a large collection of utilities for working with PacBio bas.h5 files and other common file formats.  SMRT View is an application for graphical visualization of processed and annotated sequence data, including kinetics data unique to PacBio SMRT technology.  SMRT Analysis can run in single, distributed, or mixed modes. An Amazon Web Service (AWS) cloud-based implementation is available.

For the demonstration, we will highlight an automated workflow for a mid-sized de novo genome assembly using the HGAP protocol on sequence data from Arabidopsis thaliana Ler-0.   A walkthrough of the analysis workflow and data visualization demonstrates the accessibility of state-of-the-art computational tools for non-bioinformaticians.

The software can be downloaded from the PacBio Developer’s Network website (http://www.pacbiodevnet.com).  Support for PacBio customers is available through the PacBio Customer Portal (http://www.pacbioportal.com), or GitHub (https://github.com/PacificBiosciences/SMRT-Analysis) for customers of core facilities.