• Manuals

Browse the manual

• Introduction to CLC Genomics Workbench
  • Contact information
  • System requirements
    • Limitations on maximum number of cores
  • Licenses
    • Request an evaluation license
    • Download a license using a license order ID ID
    • Import a license from a file
    • Upgrade license
    • Configure license server connection
    • Download a static license on a non-networked machine
    • Limited mode
  • About CLC Workbenches
    • New program feature request
    • Getting help
    • CLC Sequence Viewer vs. Workbenches
  • When the program is installed: Getting started
    • Quick start
    • Import of example data
  • Plugins
    • Installing plugins
    • Uninstalling plugins
    • Updating plugins
    • Resources
  • Network configuration
  • Latest improvements
• User interface
  • View Area
    • Open view
    • Show element in another view
    • Close views
    • Save changes in a view
    • Undo/Redo
    • Arrange views in View Area
    • Moving a view to a different screen
    • Side Panel
  • Zoom and selection in View Area
    • Zoom in
    • Zoom out
    • Selecting, panning and zooming
  • Toolbox and Status Bar
    • Processes
    • Toolbox
    • Status Bar
  • Workspace
    • Create Workspace
    • Select Workspace
    • Delete Workspace
  • List of shortcuts
• Data management and search
  • Navigation Area
    • Data structure
    • Create new folders
    • Sorting folders
    • Multiselecting elements
    • Moving and copying elements
    • Change element names
    • Delete, restore and remove elements
    • Show folder elements in a table
  • Customized attributes on data locations
    • Configuring which fields should be available
    • Editing lists
    • Removing attributes
    • Changing the order of the attributes
  • Filling in values
    • What happens when a clc object is copied to another data location?
    • Searching
  • Local search
    • What kind of information can be searched?
    • Quick search
    • Advanced search
    • Search index
• User preferences and settings
  • General preferences
  • Default view preferences
    • Number formatting in tables
    • Import and export Side Panel settings
  • Data preferences
  • Advanced preferences
    • Default data location
    • NCBI BLAST
  • Export/import of preferences
    • The different options for export and import
  • View settings for the Side Panel
    • Saving, removing and applying saved settings
• Printing
  • Selecting which part of the view to print
  • Page setup
    • Header and footer
  • Print preview
• Import/export of data and graphics
  • Standard import
    • Import using the import dialog
    • Import using drag and drop
    • Import using copy/paste of text
    • External files
  • Import tracks
  • Import high-throughput sequencing data
    • 454 from Roche Applied Science
    • Illumina
    • SOLiD from Life Technologies
    • Fasta read files
    • Sanger sequencing data
    • Ion Torrent PGM from Life Technologies
    • Complete Genomics
    • General notes on handling paired data
    • SAM and BAM mapping files
  • Data export
    • Export of folders and multiple elements in CLC format
    • Export of dependent elements
    • Export history
    • The CLC format
    • Backing up data from the CLC Workbench
    • Export of workflow output
  • Export graphics to files
    • Which part of the view to export
    • Save location and file formats
    • Graphics export parameters
    • Exporting protein reports
  • Export graph data points to a file
  • Copy/paste view output
• History log
  • Element history
    • Sharing data with history
• Batching and result handling
  • Batch processing
    • Batch overview
    • Batch filtering and counting
    • Setting parameters for batch runs
    • Running the analysis and organizing the results
  • How to handle results of analyses
    • Table outputs
    • Batch log
  • Working with tables
    • Filtering tables
• Workflows
  • Creating a workflow
    • Adding workflow elements
    • Configuring workflow elements
    • Locking and unlocking parameters
    • Connecting workflow elements
    • Input and output
    • Layout
    • Input modifying tools
    • Workflow validation
    • Workflow creation helper tools
    • Adding to workflows
    • Supported data flows
  • Distributing and installing workflows
    • Creating a workflow installation file
    • Installing a workflow
    • Workflow identification and versioning
    • Automatic update of workflow elements
  • Executing a workflow
• Viewing and editing sequences
  • View sequence
    • Sequence settings in Side Panel
    • Restriction sites in the Side Panel
    • Selecting parts of the sequence
    • Editing the sequence
    • Sequence region types
  • Circular DNA
    • Using split views to see details of the circular molecule
    • Mark molecule as circular and specify starting point
  • Working with annotations
    • Viewing annotations
    • Adding annotations
    • Edit annotations
    • Removing annotations
  • Element information
  • View as text
  • Sequence Lists
    • Graphical view of sequence lists
    • Sequence list table
    • Extract sequences from sequence list
• Data download
  • GenBank search
    • GenBank search options
    • Handling of GenBank search results
    • Save GenBank search parameters
  • UniProt (Swiss-Prot/TrEMBL) search
    • UniProt search options
    • Handling of UniProt search results
    • Save UniProt search parameters
  • Search for structures at NCBI
    • Structure search options
    • Handling of NCBI structure search results
    • Save structure search parameters
  • Download reference genome data
    • Selecting data types for download
  • Sequence web info
    • Google sequence
    • NCBI
    • PubMed References
    • UniProt
    • Additional annotation information
• BLAST search
  • Running BLAST searches
    • BLAST at NCBI
    • BLAST a partial sequence against NCBI
    • BLAST against local data
    • BLAST a partial sequence against a local database
  • Output from BLAST searches
    • Graphical overview for each query sequence
    • Overview BLAST table
    • BLAST graphics
    • BLAST table
    • Extracting a consensus sequence from a BLAST result
  • Local BLAST databases
    • Make pre-formatted BLAST databases available
    • Download NCBI pre-formatted BLAST databases
    • Create local BLAST databases
  • Manage BLAST databases
    • Migrating from a previous version of the Workbench
  • Bioinformatics explained: BLAST
    • Examples of BLAST usage
    • Searching for homology
    • How does BLAST work?
    • Which BLAST program should I use?
    • Which BLAST options should I change?
    • Explanation of the BLAST output
    • I want to BLAST against my own sequence database, is this possible?
    • What you cannot get out of BLAST
    • Other useful resources
• 3D Molecule Viewer
  • Importing molecule structure files
    • From the Protein Data Bank
    • From your own file system
    • BLAST search against the PDB database
    • Import issues
  • Viewing molecular structures in 3D
    • Moving and rotating
  • Customizing the visualization
    • Visualization styles and colors
    • Project settings
  • Snapshots of the molecule visualization
  • Sequences associated with the molecules
  • Troubleshooting 3D graphics errors
  • Updating old structure files
  • Protein structure alignment
    • The Align Protein Structure dialog box
    • Example: alignment of calmodulin
    • The Align Protein Structure algorithm
• General sequence analyses
  • Extract Annotations
  • Extract sequences
  • Shuffle sequence
  • Dot plots
    • Create dot plots
    • View dot plots
  • Bioinformatics explained: Dot plots
    • Realization of dot plots
    • Examples and interpretations of dot plots
  • Bioinformatics explained: Scoring matrices
    • Different scoring matrices
    • Use of scoring matrices
  • Local complexity plot
  • Sequence statistics
    • Bioinformatics explained: Protein statistics
  • Join sequences
  • Pattern Discovery
    • Pattern discovery search parameters
    • Pattern search output
  • Motif Search
    • Dynamic motifs
    • Motif search from the Toolbox
    • Java regular expressions
  • Create motif list
• Nucleotide analyses
  • Convert DNA to RNA
  • Convert RNA to DNA
  • Reverse complements of sequences
  • Reverse sequence
  • Translation of DNA or RNA to protein
    • Translate part of a nucleotide sequence
  • Find open reading frames
    • Open reading frame parameters
• Protein analyses
  • Signal peptide prediction
    • Signal peptide prediction parameter settings
    • Signal peptide prediction output
  • Bioinformatics explained: Prediction of signal peptides
    • Why the interest in signal peptides?
    • Different types of signal peptides
    • Prediction of signal peptides and subcellular localization
    • The SignalP method
    • What do the SignalP scores mean?
  • Protein charge
    • Modifying the layout
  • Transmembrane helix prediction
  • Antigenicity
    • Plot of antigenicity
    • Antigenicity graphs along sequence
  • Hydrophobicity
    • Hydrophobicity plot
    • Hydrophobicity graphs along sequence
  • Bioinformatics explained: Protein hydrophobicity
    • Hydrophobicity scales
  • Pfam domain search
    • Download of Pfam database
    • Running Pfam Domain Search
  • Secondary structure prediction
  • Protein report
    • Protein report output
  • Reverse translation from protein into DNA
    • Reverse translation parameters
  • Bioinformatics explained: Reverse translation
    • The Genetic Code
    • Solving the ambiguities of reverse translation
  • Proteolytic cleavage detection
    • Proteolytic cleavage parameters
  • Bioinformatics explained: Proteolytic cleavage
• Primers
  • Primer design - an introduction
    • General concept
    • Scoring primers
  • Setting parameters for primers and probes
    • Primer Parameters
  • Graphical display of primer information
    • Compact information mode
    • Detailed information mode
  • Output from primer design
    • Saving primers
    • Saving PCR fragments
    • Adding primer binding annotation
  • Standard PCR
    • User input
    • Standard PCR output table
  • Nested PCR
    • Nested PCR output table
  • TaqMan
    • TaqMan output table
  • Sequencing primers
    • Sequencing primers output table
  • Alignment-based primer and probe design
    • Specific options for alignment-based primer and probe design
    • Alignment based design of PCR primers
    • Alignment-based TaqMan probe design
  • Analyze primer properties
  • Find binding sites and create fragments
    • Binding parameters
    • Results - binding sites and fragments
  • Order primers
• Sequencing data analyses
  • Importing and viewing trace data
    • Scaling traces
    • Trace settings in the Side Panel
  • Trim sequences
    • Trimming using the Trim tool
    • Manual trimming
  • Assemble sequences
  • Sort Sequences By Name
  • Assemble sequences to reference
  • Add sequences to an existing contig
  • View and edit read mappings
    • View settings in the Side Panel
    • Editing the read mapping
    • Sorting reads
    • Read conflicts
    • Using the mapping
    • Extract parts of a mapping
    • Variance table
  • Reassemble contig
  • Secondary peak calling
• Cloning and cutting
  • Molecular cloning
    • Introduction to the cloning editor
    • The cloning workflow
    • Manual cloning
    • Insert restriction site
  • Gateway cloning
    • Add attB sites
    • Create entry clones (BP)
    • Create expression clones (LR)
  • Restriction site analysis
    • Dynamic restriction sites
    • Restriction site analysis from the Toolbox
  • Gel electrophoresis
    • Separate fragments of sequences on gel
    • Separate sequences on gel
    • Gel view
  • Restriction enzyme lists
    • Create enzyme list
    • View and modify enzyme list
• Sequence alignment
  • Create an alignment
    • Gap costs
    • Fast or accurate alignment algorithm
    • Aligning alignments
    • Fixpoints
  • View alignments
  • Bioinformatics explained: Sequence logo
    • Calculation of sequence logos
  • Edit alignments
    • Move residues and gaps
    • Insert gaps
    • Delete residues and gaps
    • Copy annotations to other sequences
    • Move sequences up and down
    • Delete, rename and add sequences
    • Realign selection
  • Join alignments
    • How alignments are joined
  • Pairwise comparison
    • Pairwise comparison on alignment selection
    • Pairwise comparison parameters
    • The pairwise comparison table
  • Bioinformatics explained: Multiple alignments
    • Use of multiple alignments
    • Constructing multiple alignments
• Phylogenetic trees
  • Phylogenetic tree features
  • Create Trees
    • K-mer Based Tree Construction
    • Create tree
    • Model Testing
    • Maximum Likelihood Phylogeny
    • Bioinformatics explained
  • Tree Settings
    • Minimap
    • Tree layout
    • Node settings
    • Label settings
    • Background settings
    • Branch layout
    • Bootstrap settings
    • Metadata
    • Node right click menu
  • Metadata and Phylogenetic Trees
    • Table Settings and Filtering
    • Add or modify metadata
    • Unknown metadata values
    • Selection of specific nodes
• RNA structure
  • RNA secondary structure prediction
    • Selecting sequences for prediction
    • Structure output
    • Partition function
    • Advanced options
    • Structure as annotation
  • View and edit secondary structures
    • Graphical view and editing of secondary structure
    • Tabular view of structures and energy contributions
    • Symbolic representation in sequence view
    • Probability-based coloring
  • Evaluate structure hypothesis
    • Selecting sequences for evaluation
    • Probabilities
  • Structure Scanning Plot
    • Selecting sequences for scanning
    • The structure scanning result
  • Bioinformatics explained: RNA structure prediction by minimum free energy minimization
    • The algorithm
    • Structure elements and their energy contribution
• Trimming, multiplexing and sequencing quality control
  • Trim Sequences
    • Quality trimming
    • Adapter trimming
    • Length trimming
    • Trim output
  • Demultiplex reads
  • Sequencing data quality control
    • Report contents
    • Adapters
    • Running the quality control tool
  • Merge overlapping pairs
    • Using quality scores when merging
    • Report of merged pairs
• Tracks
  • Track lists
    • Zooming and navigating track views
    • Adding, removing and reordering tracks
    • Showing a track in a table
    • Open track from a track list in table view
    • Finding annotations on the genome
    • Extract sequences from tracks
    • Creating track lists in workflows
  • Retrieving reference data tracks
  • Merging tracks
  • Converting data to tracks and back
    • Convert to tracks
    • Convert from tracks
  • Annotate and filter tracks
    • Annotate with overlap information
    • Extract reads based on overlap
    • Filter annotations on name
    • Filter Based on Overlap
  • Creating graph tracks
• Read mapping
  • Map Reads to Reference
    • Selecting reads and reference
    • Including or excluding regions (masking)
    • Mapping parameters
    • Gap placement
    • Computational requirements
    • Reference Caching
  • Mapping output options
  • Mapping reports
    • Detailed mapping report
    • Summary mapping report
  • Color space
    • Sequencing
    • Error modes
    • Mapping in color space
    • Viewing color space information
  • Mapping result
    • Mapping table
    • View settings in the Side Panel
    • Overlapping paired reads
    • Find broken pair mates
  • Local realignment
    • Method
    • Realignment of unaligned ends
    • Guided Realignment
    • Multi-pass local realignment
    • Known Limitations
    • Computational Requirements
    • How to run the Local Realignment tool
  • Merge mapping results
  • Extract consensus sequence
  • Coverage analysis
    • Running the Coverage analysis tool
• Sample Reads
  • What is Sample Reads?
  • How to run Sample Reads
• Resequencing
  • Create Statistics for Target Regions
    • Running the Create Statistics for Target Regions
    • Coverage summary report
    • Per-region statistics
    • Coverage table
  • Variant Detectors - overview
    • Differences among the variants called by the three variant callers
    • How the variant detectors work
  • Basic Variant Detection
  • Fixed Ploidy Variant Detection
    • Ploidy and sensitivity
  • Low Frequency Variant Detection
  • Variant Detectors - error model estimation
  • Variant Detectors - filters
    • General filters
    • Noise filters
  • Variant Detectors - the outputs
    • The variant track output
    • The annotated table output
    • The report
  • InDels and Structural Variants
    • How to run the InDels and Structural Variants tool
    • The Structural Variants and InDels output
    • The InDels and Structural Variants detection algorithm
    • The InDels and Structural Variants detection algorithm - Step 1: Creating Left- and Right breakpoint signatures
    • The InDels and Structural Variants detection algorithm - Step 2: Creating Structural variant signatures
    • Theoretically expected structural variant signatures
    • How sequence complexity is calculated
  • Variant data
    • Variant tracks
    • The annotated variant table
    • Variant types
    • Special notes upgrading to Genomics Workbench 7.5
  • Detailed information about overlapping paired reads
  • Annotate and filter variants
    • Filter against known variants
    • Annotating from known variants
    • Annotate with exon numbers
    • Annotate with flanking sequence
    • Filter marginal variant calls
    • Filter reference variants
  • Comparing variants
    • Compare variants within group
    • Compare sample variants
    • Fisher exact test
    • Trio analysis
    • Filter Against Control Reads
  • Predicting functional consequences
    • Amino acid changes
    • Predict splice site effect
    • GO enrichment analysis
    • Conservation score annotation
• Transcriptomics
  • RNA-Seq analysis
    • Specifying reads and reference
    • Tightly packed genes and genes in operons
    • Defining mapping options for RNA-Seq
    • Calculating expression values from RNA-Seq
    • Specifying RNA-Seq outputs
    • Interpreting the RNA-Seq analysis result
  • Small RNA analysis
    • Extract and count
    • Downloading miRBase
    • Annotating and merging small RNA samples
    • Working with the small RNA sample
    • Exploring novel miRNAs
  • Expression profiling by tags
    • Extract and count tags
    • Create virtual tag list
    • Annotate tag experiment
  • Experimental design
    • Setting up an experiment
    • Organization of the experiment table
    • Visualizing RNA-Seq read tracks for the experiment
    • Adding annotations to an experiment
    • Scatter plot view of an experiment
    • Cross-view selections
  • Working with tracks and experiments
    • Data structures for transcriptomics
  • Transformation and normalization
    • Selecting transformed and normalized values for analysis
    • Transformation
    • Normalization
  • Quality control
    • Creating box plots - analyzing distributions
    • Hierarchical clustering of samples
    • Principal component analysis
  • Statistical analysis - identifying differential expression
    • Empirical analysis of DGE
    • Tests on proportions
    • Gaussian-based tests
    • Corrected p-values
    • Volcano plots - inspecting the result of the statistical analysis
  • Feature clustering
    • Hierarchical clustering of features
    • K-means/medoids clustering
  • Annotation tests
    • Hypergeometric tests on annotations
    • Gene set enrichment analysis
  • General plots
    • Histogram
    • MA plot
    • Scatter plot
• De novo sequencing
  • De novo assembly
    • How it works
    • Resolve repeats using reads
    • Automatic paired distance estimation
    • Optimization of the graph using paired reads
    • AGP export
    • Bubble resolution
    • Converting the graph to contig sequences
    • Summary
    • Randomness in the results
    • SOLiD data support in de novo assembly
    • De novo assembly parameters
    • De novo assembly report
  • Map reads to contigs
• Epigenomics
  • ChIP-Seq Analysis
    • Quality Control of ChIP-seq data
    • Learning peak shapes
    • Applying peak shape filters to call peaks
    • Running the ChIP-Seq Analysis tool
  • Annotate with nearby gene information
• Legacy tools
  • Quality-based variant detection
    • Assessing the quality of the neighborhood bases
    • Significance of variant
    • Ploidy and genetic code
    • Reporting the variants
  • Probabilistic variant detection
    • Calculation of the prior and error probabilities
    • Calculation of the likelihood
    • Calculation of the posterior probability for each site type at each position in the genome
    • Comparison with the reference sequence and identification of candidate variants
    • Posterior filtering and reporting of variants
    • Running the variant detection
    • Setting ploidy and genetic code
    • Reporting the variants found
  • ChIP-Seq Analysis (legacy)
    • Peak finding and false discovery rates
    • Read shifting
    • Peak refinement
    • Reporting the results
• Appendix
  • Comparison of workbenches
  • Use of multi-core computers
  • Graph preferences
  • BLAST databases
    • Peptide sequence databases
    • Nucleotide sequence databases
    • Adding more databases
  • Proteolytic cleavage enzymes
  • Restriction enzymes database configuration
  • Technical information about modifying Gateway cloning sites
  • IUPAC codes for amino acids
  • IUPAC codes for nucleotides
  • Formats for import and export
    • List of bioinformatic data formats
    • List of graphics data formats
  • SAM/BAM export format specification
    • Flags
  • Gene expression annotation files and microarray data formats
    • GEO (Gene Expression Omnibus)
    • Affymetrix GeneChip
    • Illumina BeadChip
    • Gene ontology annotation files
    • Generic expression and annotation data file formats
  • Translation Tables
    • 1. Standard
    • 2. Vertebrate Mitochondrial
    • 3. Yeast Mitochondrial
    • 4. Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma
    • 5. Invertebrate Mitochondrial
    • 6. Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear
    • 9. Echinoderm Mitochondrial; Flatworm Mitochondrial
    • 10. Euplotid Nuclear
    • 11. Bacterial and Plant Plastid
    • 12. Alternative Yeast Nuclear
    • 13. Ascidian Mitochondrial
    • 14. Alternative Flatworm Mitochondrial
    • 15. Blepharisma Macronuclear
    • 16. Chlorophycean Mitochondrial
    • 21. Trematode Mitochondrial
    • 22. Scenedesmus Obliquus Mitochondrial
    • 23. Thraustochytrium Mitochondrial
    • 24. Pterobranchia Mitochondrial
    • 25. Candidate Division SR1 and Gracilibacteria
  • Custom codon frequency tables
  • Comparison of track comparison tools
  • Matrices for alignment calculation
    • PAM30 log-odds matrix
    • PAM60 log-odds matrix
    • BLOSUM42 log-odds matrix
    • BLOSUM62 log-odds matrix
    • BLOSUM80 log-odds matrix
• Bibliography

System requirements

• Windows Vista, Windows 7, Windows 8 or Windows Server 2008
• Mac OS X 10.7 or later.
• Linux: RHEL 5.0 or later. SUSE 10.2 or later. Fedora 6 or later.
• 2 GB RAM required
• 4 GB RAM recommended
• 1024 x 768 display required
• 1600 x 1200 display recommended
• Intel or AMD CPU required

  Special requirements for the 3D Molecule Viewer System requirements

  • A graphics card capable of supporting OpenGL 2.0.
  • Updated graphics drivers. Please make sure the latest driver for the graphics card is installed.

  System Recommendations

  • A discrete graphics card from either Nvidia or AMD/ATI. Modern integrated graphics cards (such as the Intel HD Graphics series) may also be used, but these are usually slower than the discrete cards.
  • A 64-bit workbench version is recommended for working with large complexes.

• Special requirements for read mapping. The numbers below give minimum and recommended memory for systems running mapping and analysis tasks. The requirements suggested are based on the genome size. Systems with less memory than specified below will benefit from installing the legacy read mapper plugin (see http://www.clcbio.com/plugins). This is slower than the standard mapper but adjusts to the amount of memory available.
  • E. coli K12 ( 4.6 megabases)
    • Minimum: 2 GB RAM
    • Recommended: 4 GB RAM
  • C. elegans ( 100 megabases) and Arabidopsis thaliana ( 120 megabases)
    • Minimum: 2 GB RAM
    • Recommended: 4 GB RAM
  • Zebrafish ( 1.5 gigabases)
    • Minimum: 2 GB RAM
    • Recommended: 4 GB RAM
  • Human ( 3.2 gigabases) and Mouse ( 2.7 gigabases)
    • Minimum: 6 GB RAM
    • Recommended: 8 GB RAM

• Special requirements for de novo assembly. De novo assembly may need more memory than stated above - this depends both on the number of reads, error profile and the complexity and size of the genome. See http://www.clcbio.com/white-paper for examples of the memory usage of various data sets.
• 64 bit computer and operating system required to use more than 2 GB RAM

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Subsections

• Limitations on maximum number of cores

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