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 Genome
- Alignments and Trees
- Create Alignment
- Create Tree
- Maximum Likelihood Phylogeny
- General Sequence Analysis
- Extract Annotations
- Extract Sequences
- Nucleotide Analysis
- Translate to Protein
- Convert DNA to RNA
- Convert RNA to DNA
- Reverse Complement Sequence
- Reverse Sequence
- Find Open Reading Frames
- Sequencing Data Analysis
- Trim Sequences
- Assemble Sequences
- Assemble Sequences to Reference
- Secondary Peak Calling
- Primers and Probes
- Find Binding Sites and Create Fragments
- BLAST
- BLAST
- BLAST at NCBI
- Download BLAST Databases
- Create BLAST Database
- Manage BLAST Databases
- NGS Core Tools
- Create Sequencing QC Report
- Merge Overlapping Pairs
- Trim Sequences
- Map Reads to Reference
- Local Realignment
- Create Detailed Mapping Report
- Merge Read Mappings
- Extract Consensus Sequence
- Process Tagged Sequences (Multiplexing)
- 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
- Probabilistic Variant Detection
- Quality-based Variant Detection
- InDels and Structural Variants
- Coverage Analysis
- Annotate from Known Variants (Annotate and Filter Variants)
- Filter against Known Variants (Annotate and Filter 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)
- Transcriptomics Analysis/ Expression Analysis
- RNA-Seq Analysis (legacy version)
- RNA-Seq Analysis
- Extract and Count (Small RNA Analysis)
- Annotate and Merge Counts (Small RNA Analysis)
- Create Histogram (General Plots)
- Epigenomics Analysis
- PeaQ Shape ChIP-Seq Analysis
- ChIP-Seq Analysis
- 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.clcbio.com/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:
http://www.clcbio.com/products/clc-genomics-server-latest-improvements/.