Preface

Preface

About this Manual

System Protection

Assistance

About this Manual

The 454 Sequencing System Software Manual describes the software package of the GS FLX, GS FLX+ and GS Junior Systems for DNA Sequencing developed by 454 Life Sciences Corporation. It is divided into 5 parts:

•	General Overview and Data File Formats

•

◦	GS Junior Sequencer (for the GS Junior System)

◦	GS Sequencer and Other On-Instrument Applications (for the GS FLX or GS FLX+ Systems)

•	Part B: GS Run Processor, GS Reporter, GS Run Browser, and GS Support Tool

•	Part C: GS De Novo Assembler, GS Reference Mapper, and SFF Tools

•	Part D: GS Amplicon Variant Analyzer

Since the software is generally common for all systems, the manual covers all applications. The only exception to this rule is the GS Sequencer or GS Junior Sequencer application, so users should make sure to refer to the manual Part A that matches their instrument.

In this documentation, the phrase “GS FLX+ System” refers to the whole system for DNA sequencing developed by 454 Life Sciences Corp., including the GS FLX+ Instrument, all the kits for the preparation, amplification and sequencing of a DNA (or RNA) sample, the methods to use the kits as described in the Manuals and Guides, and the software provided to process and analyze the data from sequencing Runs. Likewise, “GS FLX System” refers to our similar system based on the Genome Sequencer FLX Instrument (not upgraded); and “GS Junior System” to our similar lower throughput system based on the GS Junior Instrument. The phrase “454 Sequencing System” refers to the common technology that underlies all these systems. 454 Life Sciences Corporation is a Roche company.

Following an overview of data processing and analysis in the 454 Sequencing System, this manual provides a full description of these applications and commands, including how they are invoked through their Graphical User Interface (GUI) and at the UNIX command line level on the GS Junior Attendant PC or an external computing resource (a DataRig, such as the GS FLX+ Computing Station), and information on the format of the output files of all the applications.