Introduction - pb-dyim/SMRT-Analysis GitHub Wiki

This document describes the underlying command-line interface to SMRT Pipe, and is for use by bioinformaticians working with secondary analysis results.

SMRT Pipe is Pacific Biosciences’ underlying analysis framework for secondary analysis functions. SMRT Pipe is a python-based general-purpose workflow engine. It is easily extensible, and supports logging, distributed computation, error handling, analysis parameters, and temporary files.

In a typical installation of the SMRT Analysis Software, the SMRT Portal web application calls SMRT Pipe when a job is started. SMRT Portal provides a convenient and user-friendly way to analyze Pacific Biosciences’ sequencing data through SMRT Pipe. Power users will find that there is more flexibility and customization available by instead running SMRT Pipe analyses from the command line.

• The latest version of SMRT Pipe is available here.

• SMRT Pipe can also be accessed using the Secondary Analysis Web Services API. For details, see Secondary Analysis Web Services API.

Note: Throughout this documentation, the path /opt/smrtanalysis is used to refer to the installation directory for SMRT Analysis (also known as $SEYMOUR_HOME). Replace this path with the path appropriate to your installation when using this document.