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Pregap4

• Organisation of the Pregap4 Manual
• Introduction
  • Summary of the Files used and the Processing Steps
  • Introduction to the Pregap4 User Interface
    • Introduction to the Files to Process Window
    • Introduction to the Configure Modules Window
    • Introduction to the Textual Output Window
    • Introduction to Running Pregap4
  • Pregap4 Menus
    • Pregap4 File menu
    • Pregap4 Modules menu
    • Pregap4 Information source menu
    • Pregap4 Options menu
• Specifying Files to Process
• Running Pregap4
• Non Interactive Processing
• Command Line Arguments
• Configuring the Pregap4 User Interface
  • Fonts and Colours
  • Window Styles
• Configuring Modules
  • General Configuration
  • Estimate Base Accuracies
  • Phred
  • ATQA
  • Trace Format Conversion
  • Compress Trace Files
  • Initialise Experiment Files
  • Augment Experiment Files
  • Quality Clip
  • Sequencing Vector Clip
  • Cross_match
  • Cloning Vector Clip
  • Screen for Unclipped Vector
  • Screen Sequences
  • Blast Screen
  • Interactive Clipping
  • Extract Sequence
  • RepeatMasker
  • Tag Repeats
  • Mutation Detection
  • Reference Traces and Reference Sequences
  • Trace Difference
  • Heterozygote Scanner
  • Gap4 Shotgun Assembly
  • Cap2 Assembly
  • Cap3 Assembly
  • FakII Assembly
  • Phrap Assembly
  • Enter Assembly into Gap4
  • Email
  • Old Cloning Vector Clip - Obsolete
  • ALF/ABI to SCF Conversion - Obsolete
• Using Config Files
• Pregap4 Naming Schemes
  • Old Sanger Centre Naming Scheme
  • New Sanger Centre Naming Scheme
  • Writing Your Own Naming Schemes
• Pregap4 Components
• Information Sources
  • Simple Text Database
  • Experiment File Line Types
• Adding and Removing Modules
• Low Level Pregap4 Configuration
  • Low Level Global Configuration
  • Low Level Component Configuration
  • Low Level Module Configuration
    • General Configuration
    • ALF/ABI to SCF Conversion
    • Estimate Base Accuracies
    • Phred
    • ATQA
    • Compress Trace Files
    • Trace Format Conversion
    • Initialise Experiment Files
    • Augment Experiment Files
    • Uncalled Base Clip
    • Quality Clip
    • Sequencing Vector Clip
    • Cross_match
    • Cloning Vector Clip
    • Old Cloning Vector Clip
    • Screen for Unclipped Vector
    • Screen Sequences
    • Blast Screen
    • Interactive Clipping
    • Extract Sequence
    • Tag Repeats
    • RepeatMasker
    • Mutation Detection
    • Gap4 Shotgun Assembly
    • Cap2 Assembly
    • Cap3 Assembly
    • FakII Assembly
    • Phrap Assembly
    • Enter Assembly into Gap4
    • Email
    • Shutdown
• Writing New Modules
  • An Overview of a Module
  • Functions
  • Module Variables
  • Global Variables
  • Builtin Functions
  • An Example Module
• General Index
• File Index
• Variable Index
• Function Index

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This page is maintained by staden-package. Last generated on 22 October 2002.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/pregap4_unix_97.html