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• 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

Sequence alignment

CLC Genomics Workbench can align nucleotides and proteins using a progressive alignment algorithm (see Bioinformatics explained: Multiple alignments).

This chapter describes how to use the program to align sequences, and alignment algorithms in more general terms.

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Subsections

• Create an alignment
• View alignments
• Edit alignments
• Join alignments
• Pairwise comparison
• Bioinformatics explained: Multiple alignments

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