• Product manuals

Browse the manual

• Introduction to CLC Genomics Workbench
  • Contact information and citation
  • System requirements
  • Installation and startup
    • General information about installing and upgrading Workbenches
    • Installation on Microsoft Windows
    • Installation on macOS
    • Installation on Linux with an installer
    • Viewing mode
    • Safe mode
  • Workbench Licenses
    • Use QDI Licensing
    • Download a license using a license order ID
    • Import a license from a file
    • Upgrade license
    • Configure license manager connection
    • Download a static license on a non-networked machine
    • Viewing or updating license information
  • Plugins
    • Install
    • Uninstall
    • Updating plugins
  • Network configuration
• User interface
  • View Area
    • Save changes in a view
    • Undo/Redo
    • Arrange views in View Area
    • Moving a view to a different screen
    • Side Panel
  • Zoom functionality in the View Area
  • Toolbox panel
  • Processes tab and Status bar
  • Element Info view
  • History view
  • Workspace
  • List of shortcuts
• Data management and search
  • Navigation Area
    • Data structure
    • Adding and removing locations
    • Data sharing information
    • Create new folders
    • Multiselecting elements
    • Copying and moving elements and folders
    • Updating element and folder names
    • Delete, restore and remove elements
    • Show folder elements in a table
  • Working with non-CLC format files
  • Customized attributes on data locations
    • Setting custom attribute values
    • Custom attributes on elements copied to other data locations
    • Searching custom attributes
  • Searching for data in CLC Locations
    • Quick Search
    • Local Search
  • Backing up data from the CLC Workbench
  • Working with AWS S3 using the Remote Files tab
• User preferences and settings
  • General preferences
  • View preferences
  • Data preferences
  • Advanced preferences
  • Export/import of preferences
  • Side Panel view settings
• Printing
  • Selecting which part of the view to print
  • Page setup
  • Print preview
• Connections to other systems
  • CLC Server connection
    • CLC Server data import and export
  • AWS Connections
  • Public S3 buckets
• Importing data
  • Standard import
  • Import tracks
    • GFF3 format
    • VCF import
  • Import NGS Reads
    • Illumina
    • Oxford Nanopore
    • PacBio Long Reads
    • PacBio Onso
    • Element Biosciences
    • Ion Torrent
    • MGI/BGI
    • Singular Genomics
    • Ultima Genomics
    • General notes on handling paired data
    • General notes on UMIs
  • Import other high-throughput sequencing data
    • Fasta read files
    • Sanger sequencing data
    • SAM, BAM and CRAM mapping files
  • Import RNA spike-in controls
  • Import Primer Pairs
• Exporting data and graphics
  • Data export
    • Export formats
    • Export parameters
    • Specifying the exported file name(s)
    • Export of folders and data elements in CLC format
    • Export of dependent elements
    • Export of tables
    • Export in VCF format
    • GFF3 export
    • BED export
    • JSON export
    • Graphics export
    • Export history
  • Export graphics to files
    • File formats
  • Export graph data points to a file
  • Copying and pasting data from an open view
• Working with tables
  • Table view settings and column ordering
  • Filtering tables
    • Simple filtering
    • Advanced filtering
• Data download
  • Search for Sequences at NCBI
    • NCBI search options
    • Handling of NCBI search results
  • Search for PDB Structures at NCBI
    • Structure search options
    • Handling of NCBI structure search results
    • Save structure search parameters
  • Search for Sequences in UniProt (Swiss-Prot/TrEMBL)
    • UniProt search options
    • Handling of UniProt search results
  • Search for Reads in SRA
    • Searching SRA
    • Downloading reads and metadata from SRA
    • Troubleshooting SRA downloads
  • Sequence web info
• References management
  • Download Genomes
  • QIAGEN Sets
  • Reference Data Sets and defining Custom Sets
    • Copy to References
    • Export a Custom Data Set
    • Import a Custom Data Set
  • Storing, managing and moving reference data
    • Imported Data
    • Exporting reference data outside of the Reference Data Manager framework
• Running tools, handling results and batching
  • Running tools
    • Running a tool on a CLC Server
  • Handling results
  • Batch processing
• Metadata
  • Creating metadata tables
    • Importing metadata
    • Creating a metadata table directly in the Workbench
  • Associating data elements with metadata
    • Associate Data Automatically
    • Associate Data with Row
  • Working with data and metadata
    • Finding data elements based on metadata
    • Viewing metadata associations
    • Removing metadata associations
    • Identifying metadata rows without associated data
    • Editing Metadata tables
  • Moving, copying and exporting metadata
• Workflows
  • Creating and editing workflows
    • Adding elements to a workflow
    • Connecting workflow elements
    • Workflow groups
    • Adjusting the workflow layout
    • Inspecting and completing a workflow
    • Snippets in workflows
    • Customizing the Workflow Editor
  • Workflow elements
    • Anatomy of workflow elements
    • Basic configuration of workflow elements
    • Configuring Workflow Input elements
    • Configuring Workflow Output and Export elements
    • Control flow elements
    • Track lists as workflow outputs
    • Input modifying tools
    • The Configuration Editor view
  • Launching workflows individually and in batches
    • Workflow Result Metadata tables
    • Running workflows in batch mode
    • Running part of a workflow multiple times
    • Specifying reference data in the launch wizard
  • Advanced workflow batching
    • Batching workflows with more than one input changing per run
    • Multiple levels of batching
  • Template workflows
    • Import with Metadata
    • Prepare Raw Data
    • De Novo Assemble Long Reads and Polish with Short Reads
    • Identify DNA Germline Variants workflow
    • RNA-Seq and Differential Gene Expression Analysis workflow
    • Trim and Map Sanger Sequences
  • Managing workflows
    • Updating workflows
    • Workflow installation
    • Using workflow installation files
  • QIAseq Panel Analysis Assistant
    • Adding QIAseq analyses
    • Reference data for QIAseq analyses
    • Running a QIAseq analysis
    • Non-standard parameters in QIAseq analyses
    • Configuring QIAseq analyses
    • QIAseq custom panels
• Viewing and editing sequences
  • Working with sequences
    • Sequence view
    • Selecting parts of the sequence
    • Editing the sequence
    • Table view of sequences
    • Circular DNA
  • Working with sequence lists
    • Creating sequence lists
    • Sequence List view
    • Table view of sequence lists
    • Annotation Table view of sequence lists
    • Working with paired sequences in lists
  • Working with annotations
    • Viewing annotations
    • Adding annotations
    • Editing annotations
    • Removing annotations
    • Export annotations to a GFF3 format file
  • Sequence element information
  • View as text
• BLAST search
  • BLAST against local data
  • BLAST at NCBI
  • Output from BLAST searches
    • Graphical overview for each query sequence
    • Overview BLAST table
    • BLAST graphics
    • BLAST HSP table
    • BLAST hit table
    • Extracting a consensus sequence from a BLAST result
  • Local BLAST databases
    • Download NCBI pre-formatted BLAST databases
    • Make pre-formatted BLAST databases available
    • Create local BLAST databases
  • Manage BLAST databases
  • Bioinformatics explained: BLAST
    • How does BLAST work?
    • Which BLAST program should I use?
    • Which BLAST options should I change?
    • Where can I get the BLAST+ programs
    • 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
  • Customizing the visualization
    • Visualization styles and colors
    • Project settings
  • Tools for linking sequence and structure
    • Show sequence associated with molecule
    • Link sequence or sequence alignment to structure
    • Transfer annotations between sequence and structure
  • Align Protein Structure
    • Example: alignment of calmodulin
    • The Align Protein Structure algorithm
  • Generate Biomolecule
• General sequence analyses
  • Annotate with GFF/GTF/GVF files
  • Create Complexity Plot
  • Create Dot Plot
    • View dot plots
    • Bioinformatics explained: Dot plots
    • Bioinformatics explained: Scoring matrices
  • Create Sequence Statistics
    • Bioinformatics explained: Protein statistics
  • Extract Sequences
  • Join Sequences
  • Pattern Discovery
  • Shuffle Sequence
  • Motif
    • Create Motif List
    • Create Motif List from Sequences
    • Interactive motif search
    • Motif Search
    • Using motifs in sequence analysis
    • Java regular expressions
• Nucleotide analyses
  • Convert DNA to RNA
  • Convert RNA to DNA
  • Reverse complements of sequences
  • Translation of DNA or RNA to protein
  • Find open reading frames
• Protein analyses
  • Protein charge
  • Antigenicity
  • Hydrophobicity
    • Hydrophobicity graphs along sequence
    • Bioinformatics explained: Protein hydrophobicity
  • Download Pfam Database
  • Pfam domain search
  • Find and Model Structure
    • Create structure model
    • Model structure
  • Secondary structure prediction
  • Protein report
  • Reverse translation from protein into DNA
    • Bioinformatics explained: Reverse translation
  • Proteolytic cleavage detection
    • Bioinformatics explained: Proteolytic cleavage
• Primers
  • Primer design - an introduction
  • Setting parameters for primers and probes
  • Graphical display of primer information
    • Compact information mode
    • Detailed information mode
  • Output from primer design
  • Standard PCR
    • When a single primer region is defined
    • When both forward and reverse regions are defined
    • Standard PCR output table
  • Nested PCR
  • TaqMan
  • Sequencing primers
  • 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
    • Results - binding sites and fragments
  • Order primers
• Sequencing data analyses
  • Importing and viewing trace data
    • Trace settings in the Side Panel
  • Trim sequences
    • Trimming using the Trim Sequences tool
    • Manual trimming
  • Assemble sequences
  • Assemble sequences to reference
  • Sort sequences by name
  • Add sequences to an existing contig
  • View and edit contigs and read mappings
    • View settings in the Side Panel
    • Editing a contig or read mapping
    • Sorting reads
    • Read conflicts
    • Using the mapping
    • Extracting reads from mappings
    • Variance table
  • Reassemble contig
  • Secondary peak calling
  • Extract Consensus Sequence
• Cloning and restriction sites
  • Create Sequence Constructs
    • Create Sequence Constructs output
  • Homology Based Cloning
    • Working with homology based cloning
    • Adjust the homology based cloning design
    • Homology Based Cloning outputs
    • Detailed description of the Homology Based Cloning wizard
    • Working with mutations
  • Gateway cloning
    • Add attB sites
    • Create entry clones (BP)
    • Create expression clones (LR)
  • Restriction Analysis and Cloning
    • Create Enzyme List
    • Restriction Based Cloning
    • Restriction Site Analysis
    • Dynamic restriction sites
    • Insert restriction site
  • Gel electrophoresis
    • Gel view
• Sequence alignment
  • Create an alignment
    • Gap costs
    • Fast or accurate alignment algorithm
    • Redo alignments
    • Fixpoints
  • View alignments
    • Bioinformatics explained: Sequence logo
  • Edit alignments
    • Realignment
  • Join alignments
  • Pairwise comparison
    • The pairwise comparison table
  • Bioinformatics explained: Multiple alignments
• Phylogenetic trees
  • Tools for tree construction
    • K-mer Based Tree Construction
    • Create Tree
    • Model Testing
    • Maximum Likelihood Phylogeny
  • Tree Settings
    • Minimap
    • Tree layout
    • Node settings
    • Label settings
    • Background settings
    • Branch layout
    • Bootstrap settings
    • Visualizing metadata
    • Node right-click menu
  • Additional tree views
    • Tree table view
  • Bioinformatics explained
    • The phylogenetic tree
    • Substitution models and distance estimation
    • K-mer based distance estimation
    • Distance-based reconstruction methods
    • Maximum Likelihood reconstruction methods
    • Bootstrap tests
    • Scale bar
• RNA structure
  • RNA secondary structure prediction
    • Selecting sequences for prediction
    • Secondary structure prediction parameters
    • 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
• Tracks
  • Track types
  • Track lists
  • Working with tracks
    • Visualizing, zooming and navigating tracks
    • The Table view
    • The Chromosome Table view
    • Finding information in tracks
    • Extracting sequences from tracks
  • Reference data as tracks
  • Convert tracks
    • Convert from Tracks
    • Convert to Tracks
  • Graph tracks
    • Create GC Content Graph
    • Create Mapping Graph
    • Identify Graph Threshold Areas
  • Merge tracks
    • Merge Annotation Tracks
    • Merge Variant Tracks
  • Modify tracks
    • Annotate with Exon Numbers
    • Annotate with Nearby Information
    • Annotate with Overlap Information
    • Collapse Overlapping Annotations
    • Remove Information from Track
    • Resize Annotations
• Prepare sequencing data
  • QC for Sequencing Reads
    • Per-sequence analysis
    • Per-base analysis
    • Over-representation analyses
  • Trim Reads
    • Quality trimming
    • Adapter trimming
    • Trim adapter list
    • Homopolymer trimming
    • Sequence trimming
    • Sequence filtering
    • Trim output
  • Demultiplex Reads
    • Running Demultiplex Reads
    • Output from Demultiplex Reads
    • Running Demultiplex Reads in workflows
• Quality control for resequencing analysis
  • QC for Targeted Sequencing
    • Coverage summary report
    • Per-region statistics
    • Coverage table
    • Coverage graph
    • Gene coverage
  • Target Region Coverage Analysis
    • Output from Target Region Coverage Analysis
  • QC for Read Mapping
    • References
    • Mapped read statistics
    • Statistics table for each mapping
  • Whole Genome Coverage Analysis
• Read mapping
  • Map Reads to Reference
    • Selecting the reads
    • References and masking
    • Mapping parameters
    • Mapping paired reads
    • Non-specific matches
    • Gap placement
    • Mapping computational requirements
    • Reference caching
    • Mapping output options
    • Summary mapping report
  • Map Long Reads to Reference
    • Map Long Reads to Reference output
  • Reads tracks and stand-alone read mappings
    • Coloring of mapped reads
    • Reads tracks
    • Stand-alone read mapping
  • Local Realignment
    • Method
    • Realignment of unaligned ends
    • Guided realignment
    • Multi-pass local realignment
    • Known limitations
    • Computational requirements
    • Run the Local Realignment tool
  • Merge Read Mappings
  • Remove Duplicate Mapped Reads
    • Algorithm details and parameters
    • Running remove duplicate mapped reads
  • Extract Consensus Sequence
• Variant detection
  • Variant Detection tools
    • Differences in the variants called by the different tools
    • How the variant detection tools work
    • Detailed information about overlapping paired reads
  • Fixed Ploidy Variant Detection
  • Low Frequency Variant Detection
  • Basic Variant Detection
  • Variant Detection - filters
    • General filters
    • Noise filters
  • Variant Detection - the outputs
    • Variant tracks
    • The annotated variant table
    • The variant detection report
  • Fixed Ploidy and Low Frequency Detection tools: detailed descriptions
    • Variant Detection - error model estimation
    • The Fixed Ploidy Variant Detection tool: Models and methods
    • The Low Frequency Variant Detection tool: Models and methods
  • Copy Number Variant Detection
    • The Copy Number Variant Detection (Targeted) tool
    • Region-level CNV track (Region CNVs)
    • Target-level CNV track (Target CNVs)
    • Gene-level annotation track (Gene CNVs)
    • How to interpret fold-changes when the sample purity is not 100%
    • CNV results report
    • CNV algorithm report
  • Identify Known Mutations from Sample Mappings
    • Run the Identify Known Mutations from Sample Mappings tool
    • Output from the Identify Known Mutations from Sample Mappings tool
  • InDels and Structural Variants
    • Run the InDels and Structural Variants tool
    • The Structural Variants and InDels output
    • The InDels and Structural Variants detection algorithm
    • Theoretically expected structural variant signatures
    • How sequence complexity is calculated
  • Structural Variant Caller for Long Reads
    • Structural Variant Caller for Long Reads settings
    • Structural Variant Caller for Long Reads output
    • Structural Variant Caller for Long Reads algorithm
  • Detect Fusion Genes from DNA
    • Running Detect Fusion Genes from DNA
    • Output from Detect Fusion Genes from DNA
    • Filtering detected fusions
    • Fusion detection
• Resequencing analysis
  • Variant filtering
    • Filter against Known Variants
    • Filter Homozygous Reference Variants
    • Remove Variants Present in Control Reads
  • Variant annotation
    • Annotate from Known Variants
    • Annotate with Effect Scores
    • Annotate with Conservation Score
    • Annotate with Flanking Sequence
    • Annotate with Repeat and Homopolymer Information
  • Variants comparison
    • Identify Shared Variants
    • Identify Enriched Variants in Case vs Control Samples
    • Trio Analysis
  • Variant quality control
    • Create Variant Track Statistics Report
  • Functional consequences
    • Amino Acid Changes
    • Predict Splice Site Effect
    • GO Enrichment Analysis
    • Download 3D Protein Structure Database
    • Link Variants to 3D Protein Structure
  • Create Consensus Sequences from Variants
• RNA-Seq and Small RNA analysis
  • RNA-Seq normalization
  • Create Expression Browser
    • The expression browser
    • Expression browser plot
  • miRNA analysis
    • Quantify miRNA
    • Annotate with RNAcentral Accession Numbers
    • Create Combined miRNA Report
    • Extract IsomiR Counts
    • Explore Novel miRNAs
  • RNA-Seq Tools
    • RNA-Seq Analysis
    • RNA-Seq Analysis for Long Reads
    • Detect and Refine Fusion Genes
    • Import Expression Data
  • Expression Plots
    • PCA for RNA-Seq
    • Create Sample Level Heat Map for RNA-Seq
    • Create Feature Level Heat Map for RNA-Seq
    • Create K-medoids Clustering for RNA-Seq
  • Differential Expression
    • Pre-filtering data for Differential Expression
    • The GLM model
    • Differential Expression in Two Groups
    • Differential Expression for RNA-Seq
    • Output of the Differential Expression tools
    • Create Venn Diagram for RNA-Seq
    • Gene Set Test
• Microarray analysis
  • Experimental design
    • Setting up a microarray experiment
    • Organization of the experiment table
    • Adding annotations to an experiment
    • Scatter plot view of an experiment
    • Cross-view selections
  • Transformation and normalization
    • Selecting transformed and normalized values for analysis
    • Transformation
    • Normalization
  • Quality control
    • Create Box Plot
    • Hierarchical Clustering of Samples
    • Principal Component Analysis
  • Feature clustering
    • Hierarchical clustering of features
    • K-means/medoids clustering
  • Statistical analysis - identifying differential expression
    • Tests on proportions
    • Gaussian-based tests
    • Corrected p-values
    • Volcano plots - inspecting the result of the statistical analysis
  • Annotation tests
    • Hypergeometric Tests on Annotations
    • Gene Set Enrichment Analysis
  • General plots
    • Scatter plot
    • MA plot
    • Histogram
• De Novo sequencing
  • De Novo Assembly
    • The De Novo Assembly algorithm
    • Best practices
    • Randomness in the results
    • De Novo Assembly parameters
    • De Novo Assembly output
  • Map Reads to Contigs
  • De Novo Assemble Long Reads
    • De Novo Assemble Long Reads parameters
    • De Novo Assemble Long Reads output
  • Polish Contigs with Reads
    • Polish Contigs with Reads output
• Epigenomics analysis
  • Histone Chip-Seq
  • ChIP-Seq Analysis
    • Quality Control of ChIP-Seq data
    • Learning peak shapes
    • Applying peak shape filters to call peaks
    • Running the Transcription Factor ChIP-Seq tool
    • Peak track
  • Bisulfite Sequencing
    • Detecting DNA methylation
    • Map Bisulfite Reads to Reference
    • Call Methylation Levels
    • Create RRBS-fragment Track
  • Advanced Peak Shape Tools
    • Learn Peak Shape Filter
    • Apply Peak Shape Filter
    • Score Regions
• Utility tools
  • Extraction
    • Extract Annotated Regions
    • Extract Reads
  • Filtering
    • Filter Based on Name
    • Filter Based on Overlap
    • Filter on Custom Criteria
  • Renaming
    • Rename Elements
    • Rename Sequences in Lists
  • Reports
    • Combine Reports
    • Create Report from Table
    • Create Sample Report
    • Modify Report Type
  • Sequences
    • Create Sequence List
    • Download Taxonomy
    • Merge Overlapping Pairs
    • Split Sequence List
    • Subsample Sequence List
    • Update Sequence Attributes
  • Track utility tools
• Legacy tools
  • AGP export (legacy)
• Appendix
  • Use of multi-core computers
  • Graph preferences
  • 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/CRAM 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
  • 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

Viewing mode

CLC Workbenches can be run for free in Viewing Mode. Using Viewing Mode does not require a license, and can be used to view and export data. In addition, some types of data can be imported and some basic bioinformatics analysis tools are available.

Viewing Mode can be particularly useful when sharing data with colleagues or reviewers who do not have access to a Workbench license.

Data viewing

Any data type supported by the Workbench can be viewed in Viewing Mode. Plugins or modules can also be installed when in Viewing Mode, expanding the range of data types supported.

Import, export and analysis in Viewing Mode

When working in Viewing Mode, supported import and export functionality can be accessed by clicking on the Import and Export buttons in the top Toolbar, respectively. Other tools available are listed in the Workbench Tools menu (figure 1.2).

Figure 1.2: Some basic tools are available in Viewing Mode.

Starting a CLC Workbench in Viewing Mode

Click on the button labeled Viewing Mode to start the Workbench in this mode. This button is presented in various dialogs, including at the bottom of the License Assistant when a Workbench is started up and it does not (yet) have access to a valid license (figure 1.3).

Figure 1.3: Click on the Viewing Mode button, here shown at the bottom of the License Assistant, to launch the Workbench in Viewing Mode.

Starting a licensed CLC Workbench from Viewing Mode

To go from Viewing Mode to running a Workbench with full functionality:

• Open the License Manager by going to:

          Help | License Manager ()

• Click on the Update License Details button to open the License Assistant.
• Choose the relevant option to provide a license for the Workbench (see Workbench Licenses).
• Restart the Workbench when prompted.

---