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GS De Novo Assembler
GS De Novo Assembler GUI
Launching the GS De Novo Assembler GUI Application
The Main Buttons, Status Area and Progress Box
The Quick Start and Documentation Text Links
Opening a Project
Open an Existing Project
View Project Summary with the Overview Tab
Add/Remove Read Data with the Project Tab
GS Reads, FASTA and FASTQ Reads Sub-Tabs
Removing Read Data from the Project Sub-Tabs
Specifying Multiplex Identifiers (MIDs)
Customize Project with the Parameters Tab
Genomic Project Input Sub-Tab
Project Computation Sub-Tab
Genomic Project Output Sub-Tab
cDNA Project Input Sub-Tab
cDNA Project Output Sub-Tab
Computing the Assembly
Re-Computing an Assembly
Stopping an Assembly Computation
Information Updated when Assembly Completes
Viewing Assembly Output with the Result Files Tab
Viewing Contigs with the Alignment Results Tab
The Flowgrams Tab
Project Error Indicators
The GS De Novo Assembler Command Line Interface
Working with Project Folders and Data Files
One-Step Assembly: the runAssembly Command
Incremental Assembly: the newAssembly and Related Commands
GS De Novo Assembler cDNA / Transcriptome Options
GS De Novo Assembler Output
GS De Novo Assembler cDNA / Transcriptome Output
GS Reference Mapper
GS Reference Mapper GUI
Launching the GS Reference Mapper GUI
The Main Buttons, Status Area and Progress Box
The Quick Start and Documentation Text Links
Opening a Project
Open an Existing Project
View Project Summary with the Overview Tab
Add/Remove Read Data and References with the Project Tab
GS Reads, References, FASTA and FASTQ Reads Sub-Tabs
Removing Read or Reference Data from the project Sub-Tabs
Specifying Multiplex Identifiers (MIDs)
Customize Project with the Parameters Tab
Genomic Project Input Sub-Tab
Project Computation Sub-Tab
Project Output Sub-Tab
cDNA Project Input Sub-Tab
Computing the Mapping
Re-Computing a Mapping
Stopping a Mapping Computation
Information Updated when Mapping Completes
Viewing Mapping Output with the Result Files Tab
Using the Variants Tab
The HC Diffs Sub-Tab
The HC Structural Rearrangements Sub-Tab
The HC Structural Variants Sub-Tab
Profile Tab
Viewing Reads Mapped to the Reference with the Alignment Results Tab
The Flowgrams Tab
Project Error Indicators
GS Reference Mapper Command Line Interface
Working with Project Folders and Data Files
One-Step Mapping: the runMapping Command
Incremental Mapping: the newMapping and Related Commands
GS Reference Mapper cDNA / Transcriptome Options
Annotation Input Files for Mapping Transcriptomes
GS Reference Mapper Output
GS Reference Mapper cDNA / Transcriptome Output
SFF Tools Commands
sfffile
Using sfffile for Evaluation of Individual Reads
Using sfffile to Extract Read Subsets
sffinfo
sff2scf
fnafile
sffrescore
GS De Novo Assembler and GS Reference Mapper Appendices
Options Specific to Assembly
Options Specific to Mapping
Options for the addRun Command
Mutually Exclusive Options for Assembly and Mapping Commands
Serial I/O
Options for Serial I/O
Guidelines for Use
Multiplex Identifiers
The MIDConfig.parse File
Paired End Libraries in the 454 Sequencing System
Ends of Paired End Reads Shorter Than 50 bp (Tags)
Paired End Library Span Estimation
True Pairs and False Pairs
Trimming and Screening Files
Annotation File Formats
refGene.txt File Format
snp130.txt File Format
Accno Renaming File
The –urt option: Use Read Tips
Assembling with FASTA Reads Obtained Using the Sanger Sequencing Method
Simple Sanger Reads
Sanger Reads with available Quality Scores
Sanger Read Annotations
Recommended Method for Including Sanger Reads
Using the Flowgrams Tab
Project Error Indicators
Types of Structural Rearrangements
Deletion
Insertion
Substitution
Inversion
Duplication, Tandem (May or May Not Be Inverted)
Duplication, Interspersed (May or May Not Be Inverted)
Translocation (May or May Not Be Inverted)
Fusion
Exon Splice
Target Regions and Extended Target Regions
cDNA / Transcriptome Sequencing Appendix
Transcriptome Assembly Concepts
Rules for Path Traversal of Contigs in an Isogroup
Transcriptome Mapping Concepts
Mapping cDNA Reads to a Genomic Reference
Reference Type Auto Detection
Using GOLDENPATH
Not Using GOLDENPATH
Glossary