CLC Genomics Server
The CLC Genomics Server is shipped with the following tools and analyses that can all be started from CLC Genomics Workbench and CLC Server Command Line Tools:
- Import
- Export
- Search for Reads in SRA
- Download Genomes and References management
- Classical Sequence Analysis
- Create Alignment
- K-mer Based Tree Construction
- Create Tree
- Model Testing
- Maximum Likelihood Phylogeny
- Extract Sequences
- Motif Search
- Translate to Protein
- Convert DNA to RNA
- Convert RNA to DNA
- Reverse Complement Sequence
- Find Open Reading Frames
- Download Pfam Database
- Pfam Domain Search
- Find and Model Structure
- Molecular Biology Tools
- Trim Sequences
- Assemble Sequences
- Assemble Sequences to Reference
- Secondary Peak Calling
- Find Binding Sites and Create Fragments
- Add attB Sites
- Create Entry clone (BP)
- Create Expression clone (LR)
- BLAST
- BLAST
- BLAST at NCBI
- Download BLAST Databases
- Create BLAST Database
- Prepare Sequencing Data
- QC for Sequencing Reads
- Trim Reads
- Demultiplex Reads
- Quality Control
- QC for Targeted Sequencing
- Target Region Coverage Analysis
- QC for Read Mapping
- Whole Genome Coverage Analysis
- Combine Reports
- Create Sample Report
- Resequencing Analysis
- Map Reads to Reference
- Local Realignment
- Merge Read Mappings
- Remove Duplicate Mapped Reads
- Extract Consensus Sequence
- Create Consensus Sequences from Variants
- Basic Variant Detection
- Fixed Ploidy Variant Detection
- Low Frequency Variant Detection
- InDels and Structural Variants
- Identify Known Mutations from Mappings
- Copy Number Variant Detection (CNVs)
- Filter against Known Variants
- Remove Marginal Variants
- Remove Homozygous Reference Variants
- Remove Variants Present in Control Reads
- Annotate from Known Variants
- Remove Information from Variants
- Annotate with Conservation Scores
- Annotate with Exon Numbers
- Annotate with Flanking Sequences
- Annotate with Repeat and Homopolymer Information
- Identify Enriched Variants in Case vs Control Samples
- Identify Shared Variants
- Trio Analysis
- Create Variant Track Statistics Report
- Amino Acid Changes
- Predict Splice Site Effect
- GO Enrichment Analysis
- Download 3D Protein Structure Database
- Link Variants to 3D Protein Structure
- RNA-Seq and Small RNA Analysis
- Create Expression Browser
- Quantify miRNA
- Annotate with RNAcentral Accession Numbers
- Create Combined miRNA Report
- Extract IsomiR Counts
- RNA-Seq Analysis
- Detect and Refine Fusion Genes
- PCA for RNA-Seq
- Create Heat Map for RNA-Seq
- Create K-medoids Clustering for RNA-Seq
- Differential Expression in Two Groups
- Differential Expression for RNA-Seq
- Create Venn Diagram for RNA-Seq
- Gene Set Test
- Microarray Analysis
- Create Box Plot
- Principal Component Analysis
- Proportion-based Statistical Analysis
- Gaussian Statistical Analysis
- Create MA Plot
- Create Scatter Plot
- Create Histogram
- Epigenomics Analysis
- Histone ChiP-Seq
- Transcription Factor ChIP-Seq
- Annotate with Nearby Gene Information
- Map Bisulfite Reads to Reference
- Call Methylation Levels
- Create RRBS-fragment Track
- Learn Peak Shape Filter
- Apply Peak Shape Filter
- Score Regions
- De Novo Sequencing
- De Novo Assembly
- Map Reads to Contigs
- Utility Tools
- Extract Annotated Regions
- Merge Overlapping Pairs
- Extract Reads
- Merge Annotation Tracks
- Merge Variant Tracks
- Convert to Tracks
- Convert from Tracks
- Filter on Custom Criteria
- Annotate with Overlap Information
- Filter Annotations on Name
- Filter Based on Overlap
- Create GC Content Graph
- Create Mapping Graph
- Identify Graph Threshold Areas
- Update Sequence Attributes in Lists
- Split Sequence List
- Subsample Sequence List
- Rename Elements
- Rename Sequences in Lists
- Legacy Tools
- QIAGEN GeneReader Sequencing Import (legacy)
The functionality of the CLC Genomics Server can be extended by installation of Server plugins. This is described further in Server plugins
Latest improvements
CLC Genomics Server is under constant development and improvement. A detailed list that includes a description of new features, improvements, bugfixes, and changes for the current version of CLC Genomics Server can be found at: