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Introduction to CLC Genomics Workbench
- Contact information and citation
- Download and installation
- System requirements
  - Limitations on maximum number of cores
- Workbench Licenses
- Plugins
- Network configuration
User interface
- View Area
- Zoom functionality in the View Area
- Toolbox and Favorites tabs
  - Toolbox tab
  - Favorites tab
- Processes tab and Status bar
- History and Element Info views
- Workspace
- List of shortcuts
Data management and search
- Navigation Area
- Working with non-CLC format files
- Customized attributes on data locations
- Searching for data in CLC Locations
  - Quick Search
  - Local Search
- Backing up data from the CLC Workbench
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
Import of data and graphics
- Standard import
- Import tracks
  - GFF3 format
  - VCF import
- Import NGS Reads
- Import other high-throughput sequencing data
- Import RNA spike-in controls
- Import Primer Pairs
Export of data and graphics
- Data export
- Export graphics to files
  - File formats
- Export graph data points to a file
- Copy/paste view output
Working with tables
- Table view settings and column ordering
- Filtering tables
Data download
- Search for Sequences at NCBI
  - NCBI search options
  - Handling of NCBI search results
- Search for PDB Structures at NCBI
- Search for Sequences in UniProt (Swiss-Prot/TrEMBL)
  - UniProt search options
  - Handling of UniProt search results
- Search for Reads in SRA
- Sequence web info
References management
- Download Genomes
- QIAGEN Sets
- Reference Data Sets and defining Custom Sets
- 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
- Moving, copying and exporting metadata
Workflows
- Creating and editing workflows
- Workflow elements
- Launching workflows individually and in batches
- Advanced workflow batching
  - Batching workflows with more than one input changing per run
  - Multiple levels of batching
- Template workflows
- Managing workflows
- QIAseq Panel Analysis Assistant
Viewing and editing sequences
- Sequence Lists
- View sequences
- Working with annotations
- Element information
- View as text
BLAST search
- Running BLAST searches
  - BLAST at NCBI
  - BLAST against local data
- Output from BLAST searches
- Local BLAST databases
- Manage BLAST databases
- Bioinformatics explained: BLAST
3D Molecule Viewer
- Importing molecule structure files
- Viewing molecular structures in 3D
- Customizing the visualization
  - Visualization styles and colors
  - Project settings
- Tools for linking 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 file
- Extract sequences
- Shuffle sequence
- Dot plots
- Local complexity plot
- Sequence statistics
  - Bioinformatics explained: Protein statistics
- Join Sequences
- Pattern discovery
  - Pattern discovery search parameters
  - Pattern search output
- Motif Search
- Create motif list
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
  - 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
- Standard PCR
- Nested PCR
- TaqMan
- Sequencing primers
- Alignment-based primer and 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
  - Trace settings in the Side Panel
- Trim sequences
  - Trimming using the Trim 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
- Reassemble contig
- Secondary peak calling
- Extract Consensus Sequence
Cutting and cloning
- Restriction site analyses
- Restriction enzyme lists
- Restriction Based Cloning
- Homology Based Cloning
- Gateway cloning
- Gel electrophoresis
  - Gel view
Sequence alignment
- Create an alignment
- View alignments
  - Bioinformatics explained: Sequence logo
- Edit alignments
  - Realignment
- Join alignments
- Pairwise comparison
  - The pairwise comparison table
  - Bioinformatics explained: Multiple alignments
Phylogenetic trees
- K-mer Based Tree Construction
- Create tree
- Model Testing
- Maximum Likelihood Phylogeny
  - Bioinformatics explained
- Tree Settings
- Metadata and phylogenetic trees
RNA structure
- RNA secondary structure prediction
- View and edit secondary structures
- 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
- Reference data as tracks
- Merge Annotation Tracks
- Merge Variant Tracks
- Track Conversion
  - Convert to Tracks
  - Convert from Tracks
- Annotate and Filter
- Graphs
Prepare sequencing data
- QC for Sequencing Reads
- Trim Reads
- Demultiplex Reads
Quality control for resequencing analysis
- QC for Targeted Sequencing
- Target Region Coverage Analysis
  - Output from Target Region Coverage Analysis
- QC for Read Mapping
- Whole Genome Coverage Analysis
Read mapping
- Map Reads to Reference
- Reads tracks and stand-alone read mappings
- Local Realignment
- Merge Read Mappings
- Remove Duplicate Mapped Reads
  - Algorithm details and parameters
  - Running remove duplicate mapped reads
- Extract Consensus Sequence
Variant detection
- Variant Detection tools
- Fixed Ploidy Variant Detection
- Low Frequency Variant Detection
- Basic Variant Detection
- Variant Detection - filters
  - General filters
  - Noise filters
- Variant Detection - the outputs
- Fixed Ploidy and Low Frequency Detection tools: detailed descriptions
- Copy Number Variant Detection
- 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
Resequencing analysis
- Variant filtering
- Variant annotation
- Variants comparison
- Variant quality control
  - Create Variant Track Statistics Report
- Functional consequences
- 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
- RNA-Seq Tools
  - RNA-Seq Analysis
  - Detect and Refine Fusion Genes
- Expression Plots
- Differential Expression
Microarray analysis
- Experimental design
- Transformation and normalization
- Quality control
- Feature clustering
  - Hierarchical clustering of features
  - K-means/medoids clustering
- Statistical analysis - identifying differential expression
- Annotation tests
  - Hypergeometric Tests on Annotations
  - Gene Set Enrichment Analysis
- General plots
De Novo sequencing
- The CLC de novo assembly algorithm
- De Novo Assembly
- Map Reads to Contigs
Epigenomics analysis
- Histone Chip-Seq
- ChIP-Seq Analysis
- Bisulfite Sequencing
- Advanced Peak Shape Tools
Utility tools
- Extract Annotated Regions
- Extract Reads
- Filter on Custom Criteria
- Merge Overlapping Pairs
- Combine Reports
  - Combine Reports output
- Create Sample Report
  - Create Sample Report output
- Modify Report Type
  - Modifying report types in workflows
- Track tools
- Create Sequence List
- Update Sequence Attributes in Lists
- Split Sequence List
- Subsample Sequence List
- Rename Elements
- Rename Sequences in Lists
Appendix
- Use of multi-core computers
- Graph preferences
- BLAST 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/CRAM export format specification
  - Flags
- Gene expression annotation files and microarray data formats
- Translation Tables
- Custom codon frequency tables
- Comparison of track comparison tools
- Matrices for alignment calculation
Bibliography

Sequence data formats

Sequence data formats that can be imported using Standard Import are listed in the table below.

Note: There are dedicated import tools for sequence data types not listed in the table below, such as high-throughput sequencing data from Illumina, IonTorrent and other vendors, as well as high-throughput fasta and trace files. See Import high-throughput sequencing data.

File type	Suffix	Import	Export	Description
AB1	.ab1	X		Including chromatograms
ABI	.abi	X		Including chromatograms
CLC	.clc	X	X	Rich format including all information
Clone manager	.cm5	X		Clone manager sequence format
DNAstrider	.str/.strider	X	X
DS Gene	.bsml	X
EMBL	.emb/.embl	X	X	Rich information incl. annotations (nucs only)
FASTA	.fa/.fsa/.fasta	X	X	Simple format, name & description
FASTQ	.fastq	X	X	Simple format, name & description
GenBank	.gbk/.gb/.gp/.gbff	X	X	Rich information incl. annotations
Gene Construction Kit	.gcc	X
Lasergene	.pro/.seq	X
Nexus	.nxs/.nexus	X	X
Phred	.phd	X		Including chromatograms
PIR (NBRF)	.pir	X	X	Simple format, name & description
Raw sequence	any	X		Only sequence (no name)
SCF2	.scf	X		Including chromatograms
SCF3	.scf	X	X	Including chromatograms
Sequence Comma separated values	.csv	X	X	Simple format. One seq per line: name, description(optional), sequence
Staden	.sdn	X
Swiss-Prot	.swp	X	X	Rich information incl. annotations (only peptides)
Tab delimited text	.txt		X	Annotations in tab delimited text format

Additional notes about working with trace data

When importing trace data, the called bases in the file are imported and the chromatogram information associated with the called bases is imported. If the base calls within the file have already been trimmed, the part of the chromatogram not associated with base calls will not be imported.
The Trim Sequences tool, described in Trim sequences, adds annotations to trimmed regions. When exporting to fasta format, there is an option to remove sequence ends covered by Trim annotations.