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
- Download Reference Genome Data
- Search for Reads in SRA
- Classical Sequence Analysis
- Create Alignment (Alignments and Trees)
- K-mer Based Tree Construction (Alignments and Trees)
- Create Tree (Alignments and Trees)
- Model Testing (Alignments and Trees)
- Maximum Likelihood Phylogeny (Alignments and Trees)
- Extract Annotations (General Sequence Analysis)
- Extract Sequences (General Sequence Analysis)
- Motif Search (General Sequence Analysis)
- Translate to Protein (Nucleotide Analysis)
- Convert DNA to RNA (Nucleotide Analysis)
- Convert RNA to DNA (Nucleotide Analysis)
- Reverse Complement Sequence (Nucleotide Analysis)
- Reverse Sequence (Nucleotide Analysis)
- Find Open Reading Frames (Nucleotide Analysis)
- Download Pfam Database (Protein Analysis)
- Pfam Domain Search (Protein Analysis)
- Molecular Biology Tools
- Assemble Sequences (Sequencing Data Analysis)
- Assemble Sequences to Reference (Sequencing Data Analysis)
- Secondary Peak Calling (Sequencing Data Analysis)
- Find Binding Sites and Create Fragments (Primers and Probes)
- Add attB Sites (Cloning and Restriction Sites - Gateway Cloning)
- Create Entry clone (BP) (Cloning and Restriction Sites - Gateway Cloning)
- Create Expression clone (LR) (Cloning and Restriction Sites - Gateway Cloning)
- BLAST
- BLAST
- BLAST at NCBI
- Download BLAST Databases
- Create BLAST Database
- NGS Core Tools
- Sample Reads
- Create Sequencing QC Report
- Merge Overlapping Pairs
- Trim Reads
- Demultiplex Reads
- Map Reads to Reference
- Local Realignment
- Create Detailed Mapping Report
- Merge Read Mappings
- Extract Consensus Sequence
- Track Tools
- Convert to Tracks
- Convert from Tracks
- Merge Annotation Tracks
- Annotate with Overlap Information (Annotate and Filter)
- Extract Reads Based on Overlap (Annotate and Filter)
- Filter Annotations on Name (Annotate and Filter)
- Filter Based on Overlap (Annotate and Filter)
- Create GC Content Graph Tracks (Graphs)
- Create Mapping Graph Tracks (Graphs)
- Identify Graph Threshold Areas(Graphs)
- Resequencing Analysis
- Create Statistics for Target Regions
- Identify Known Mutations from Sample Mappings
- InDels and Structural Variants
- Coverage Analysis
- Basic Variant Detection (Variant Detectors)
- Fixed Ploidy Variant Detection (Variant Detectors)
- Low Frequency Variant Detection (Variant Detectors)
- Annotate from Known Variants (Annotate and Filter Variants)
- Filter against Known Variants (Annotate and Filter Variants)
- Identify Candidate Variants
- Annotate with Exon Numbers (Annotate and Filter Variants)
- Annotate with Flanking Sequences (Annotate and Filter Variants)
- Filter Marginal Variant Calls (Annotate and Filter Variants)
- Filter Reference Variants (Annotate and Filter Variants)
- Compare Sample Variant Tracks (Compare Variants)
- Compare Variants within Group (Compare Variants)
- Fisher Exact Test (Compare Variants)
- Trio Analysis (Compare Variants)
- Filter against Control Reads (Compare Variants)
- GO Enrichment Analysis (Functional Consequences)
- Amino Acid Changes (Functional Consequences)
- Annotate with Conservation Score (Functional Consequences)
- Predict Splice Site Effect (Functional Consequences)
- Link Variants to 3D Protein Structure (Functional Consequences)
- Download 3D Protein Structure Database (Functional Consequences)
- RNA-Seq Analysis
- RNA-Seq Analysis (RNA-Seq Analysis)
- PCA for RNA-Seq
- Differential Expression for RNA-Seq
- Create Heat Map for RNA-Seq
- Create Expression Browser
- Create Venn Diagram for RNA-Seq
- Gene Set Test
- Generate combined RNA-Seq Report
- Microarray and Small RNA Analysis
- Create Track from Experiment
- Extract and Count (Small RNA Analysis)
- Annotate and Merge Counts (Small RNA Analysis)
- Create Box Plot (Quality Control)
- Hierarchical Clustering of Samples (Quality Control)
- Principal Component Analysis (Quality Control)
- Empirical Analysis of DGE (Statistical Analysis)
- Proportion-based Statistical Analysis (Statistical Analysis)
- Gaussian Statistical Analysis (Statistical Analysis)
- Create MA Plot (General Plots)
- Create Scatter Plot (General Plots)
- Histogram (General Plots)
- Epigenomics Analysis
- Transcription Factor ChIP-Seq
- Annotate with Nearby Gene Information
- De Novo Sequencing
- De Novo Assembly
- Map Reads to Contigs
The functionality of the CLC Genomics Server can be extended by installation of Server plugins. The available plugins can be found at http://www.qiagenbioinformatics.com/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:
http://www.qiagenbioinformatics.com/products/clc-genomics-server/latest-improvements/current-line/.