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 Annotations
- 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
- Molecular Biology Tools
- 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
- Track Tools
- Merge Annotation Tracks
- Convert to Tracks
- Convert from Tracks
- Remove Homozygous Reference Variants
- Annotate with Overlap Information
- Filter Annotations on Name
- Filter Based on Overlap
- Create GC Content Graph Tracks
- Create Mapping Graph Tracks
- Identify Graph Threshold Areas
- Prepare Sequencing Data
- QC for Sequencing Reads
- Trim Reads
- Demultiplex Reads
- Resequencing Analysis
- Map Reads to Reference
- Local Realignment
- Merge Read Mappings
- Remove Duplicate Mapped Reads
- Extract Consensus Sequence
- Identify Known Mutations from Sample Mappings
- Basic Variant Detection (Variant Detectors)
- Fixed Ploidy Variant Detection (Variant Detectors)
- Low Frequency Variant Detection (Variant Detectors)
- Copy Number Variant Detection (CNVs)
- InDels and Structural Variants
- QC for Targeted Sequencing
- QC for Read Mapping
- Whole Genome Coverage Analysis
- Filter on Custom Criteria
- Filter against Known Variants
- Remove Marginal 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
- Identify Shared Variants
- Identify Enriched Variants in Case vs Control Samples
- Trio Analysis
- Amino Acid Changes
- Predict Splice Site Effect
- GO Enrichment Analysis
- Download 3D Protein Structure Database
- Link Variants to 3D Protein Structure
- RNA-Seq Analysis
- RNA-Seq Analysis and Small RNA Analysis
- PCA for RNA-Seq
- Differential Expression in Two Groups
- Differential Expression for RNA-Seq
- Create Heat Map for RNA-Seq
- Create Expression Browser
- Create Venn Diagram for RNA-Seq
- Gene Set Test
- Microarray Analysis
- Create Box Plot
- Hierarchical Clustering of Samples
- Principal Component Analysis
- Empirical Analysis of DGE
- Proportion-based Statistical Analysis
- Gaussian Statistical Analysis
- Create MA Plot
- Create Scatter Plot
- Create Histogram
- Epigenomics Analysis
- Transcription Factor ChIP-Seq
- Annotate with Nearby Gene Information
- Map Bisulfite Reads to Reference
- Call Methylation Level
- Create RRBS-fragment Track
- De Novo Sequencing
- De Novo Assembly
- Map Reads to Contigs
- Utility Tools
- Extract Annotations
- Sample Reads
- Extract Reads
- Merge Overlapping Pairs
- Legacy Tools
- Compare Sample Variant Tracks
- Remove Reference Variants
- Roche 454
- Create Combined RNA-Seq Report
- Create Track from Experiment
- Extract and Count
- Annotate and Merge Counts
The functionality of the CLC Genomics Server can be extended by installation of Server plugins. The available plugins can be found at https://digitalinsights.qiagen.com/products-overview/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: