Manual
User Manual:
Open the PDF directly: View PDF
Page Count: 654 [warning: Documents this large are best viewed by clicking the View PDF Link!]
- Preface
- Next generation assembly editing with Gap5
- Gap5 Databases
- Contig Selector / Comparator
- Template Display
- Editing in Gap5
- Moving the visible segment of the contig
- Names
- Editing
- Cut and Paste Control of Sequence
- Selecting Sequences
- Annotations
- Searching
- Search by Annotation Comments
- Search by Tag Type
- Search by Padded Position
- Search by Unpadded Position
- Search by Sequence
- Search by Reading Name
- Search by Reference InDel
- Search by Consensus Quality
- Search by Consensus Discrepancy
- Search by Consensus Heterozygosity
- Search by Low Coverage
- Search by High Coverage
- The Settings Menu
- Primer Selection
- Traces
- The Editor Information Line
- The Join Editor
- Using Several Editors at Once
- Quitting the Editor
- Summary
- Plotting Restriction Enzymes
- Importing and Exporting Data
- Finding Sequence Matches
- Checking Assemblies and Removing Readings
- Removing Readings and Breaking Contigs
- Tidying up alignments
- Calculating Consensus Sequences
- Other Miscellany
- Sequence assembly and finishing using Gap4
- Organisation of the gap4 Manual
- Introduction
- Contig Selector
- Contig Comparator
- Contig Overviews
- Editing in Gap4
- Moving the visible segment of the contig
- Names
- Editing
- Selections
- Annotations
- Searching
- Search by Position
- Search by Problem
- Search by Annotation Comments
- Search by Tag Type
- Search by Sequence
- Search by Quality
- Search by Consensus Quality
- Search by file
- Search by Reading Name
- Search by Edit
- Search by Evidence for Edit (1)
- Search by Evidence for Edit (2)
- Search by Discrepancies
- Search by Consensus Discrepancies
- The Commands Menu
- The Settings Menu
- Status Line
- Trace Display
- Auto-display Traces
- Show Read-pair Traces
- Auto-diff Traces
- Y scale differences
- Consensus Algorithm
- Group Readings
- Highlight Disagreements
- Compare Strands
- Toggle auto-save
- 3 Character Amino Acids
- Show Reading and Consensus Quality
- Show edits
- Show Unpadded Positions
- Show Template Names
- Set Active Tags
- Set Output List
- Set Default Confidences
- Set or unset saving of undo
- Removing Readings
- Primer Selection
- Traces
- Reference Sequence and Traces
- Template Status Codes
- The Editor Information Line
- The Join Editor
- Using Several Editors at Once
- Quitting the Editor
- Editing Techniques
- Summary
- Assembling and Adding Readings to a Database
- Ordering and Joining Contigs
- Checking Assemblies and Removing Readings
- Removing Readings and Breaking Contigs
- Finishing Experiments
- Calculating Consensus Sequences
- Miscellaneous functions
- Results Manager
- Lists
- Notes
- Gap4 Database Files
- Copy Readings
- Check Database
- Doctor Database
- Configuring
- Command Line Arguments
- Searching for point mutations using pregap4 and gap4
- Introduction to mutation detection
- Mutation Detection Programs
- Mutation Detection Reference Data
- Reference Sequences
- Reference Traces
- Using The Template Display With Mutation Data
- Configuring The Gap4 Editor For Mutation Data
- Using The Gap4 Editor With Mutation Data
- Processing Batches Of Mutation Data Trace Files
- Processing Batches Of Mutation Data Trace Files Using Pregap4
- Configuration Of Pregap4 For Mutation Data
- Discussion Of Mutation Data Processing Methods
- Introduction to mutation detection
- Preparing readings for assembly using pregap4
- Organisation of the Pregap4 Manual
- Introduction
- Specifying Files to Process
- Running Pregap4
- Configuring the Pregap4 User Interface
- Configuring Modules
- General Configuration
- Estimate Base Accuracies
- Phred
- ATQA
- Trace Format Conversion
- 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
- Mutation Scanner
- Gap4 Shotgun Assembly
- Cap2 Assembly
- Cap3 Assembly
- FakII Assembly
- Phrap Assembly
- Enter Assembly into Gap4
- Old Cloning Vector Clip - Obsolete
- ALF/ABI to SCF Conversion - Obsolete
- Using Config Files
- Pregap4 Naming Schemes
- Pregap4 Components
- Information Sources
- 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
- 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
- Shutdown
- Writing New Modules
- Marking poor quality and vector segments of readings
- Screening Against Vector Sequences
- Screening Readings for Contaminant Sequences
- Viewing and editing trace data using trev
- Analysing and comparing sequences using spin
- Organisation of the Spin Manual
- Introduction
- Spin's Analytical Functions
- Spin Comparison Functions
- Controlling and Managing Results
- The Spin User Interface
- Controlling and Managing Results
- Reading and Managing Sequences
- User Interface
- File Formats
- SCF
- ZTR
- Header
- Chunk Format
- Data format 0 - Raw
- Data format 1 - Run Length Encoding
- Data format 2 - ZLIB
- Data format 64/0x40 - 8-bit delta
- Data format 65/0x41 - 16-bit delta
- Data format 66/0x42 - 32-bit delta
- Data format 67-69/0x43-0x45 - reserved
- Data format 70/0x46 - 16 to 8 bit conversion
- Data format 71/0x47 - 32 to 8 bit conversion
- Data format 72/0x48 - "follow" predictor
- Data format 73/0x49 - floating point 16-bit chebyshev polynomial predictor
- Data format 74/0x4A - integer based 16-bit chebyshev polynomial predictor
- Chunk Types
- Text Identifiers
- References
- Experiment File
- Restriction Enzyme File
- Vector_primer File
- Vector Sequence Format
- Man Pages
- References
- General Index
- File Index
- Variable Index
- Function Index