Biomedical Genomics Server Extension
A CLC Genomics Server with the Biomedical Genomics Server Extension is shipped with the tools and analyses listed below. These can all be started from the Biomedical Genomics Workbench or by using the CLC Server Command Line Tools.
- Import
- Export
- Download Reference Genome Data
- Search for Reads in SRA
- Genome Browser
- Create GC Content Graph (Graphs)
- Create Mapping Graph (Graphs)
- Identify Graph Threshold Area (Graphs)
- Quality Control
- QC for Sequencing Reads
- QC for Target Sequencing
- QC for Read Mapping
- Preparing Raw Data
- Merge Overlapping Pairs
- Trim Reads
- Demultiplex reads
- Resequencing Analysis
- Identify Known Mutations from Sample Mappings
- Extract Reads Based on Overlap
- Map Reads to Reference
- Local Realignment
- Merge Read Mappings
- Copy Number Variant Detection
- Remove Duplicate Mapped Reads
- Indels and Structural Variants
- Whole Genome Coverage Analysis
- Basic Variant Detection (Variant Detectors)
- Fixed Ploidy Variant Detection (Variant Detectors)
- Low Frequency Variant Detection (Variant Detectors)
- Add Information to Variants
- Add Information from Variant Databases
- Add Conservation Scores
- Add Exon Number
- Add Flanking Sequence
- Add Fold Changes
- Add information about Amino Acids Changes
- Add Information from Genomic Regions
- Add Information from Overlapping Genes
- Link Variants to 3D Protein Structure
- Download 3D Protein Structure Database
- Add Information from 1000 Genomes Project (From Databases)
- Add Information from COSMIC (From Databases)
- Add Information from Clinvar (From Databases)
- Add Information from Common dbSNP (From Databases)
- Add Information from Hapmap (From Databases)
- Add Information from dbSNP (From Databases)
- Remove Variants
- Remove Variants Found in External Databases
- Remove Variants Not Found in External Databases
- Remove False Positive
- Remove Germline Variants
- Remove Reference Variants
- Remove Variants Inside Genome Regions
- Remove Variants Outside Genome Regions
- Remove Variants Outside Targeted Regions
- Remove Variants Found in 1000 Genomes Project (From Databases)
- Remove Variants Found in Common dbSNP (From Databases)
- Remove Variants Found in Hapmap (From Databases)
- Add Information to Genes
- Add Information from Overlapping Variants
- Compare Samples
- Compare Shared Variants Within a Group of Samples
- Identify Enriched Variants in Case vs Control Group
- Trio Analysis
- Identify Candidate Variants
- Identify Candidate Variants
- Remove Information from Variants
- Identify Variants with Effect on Splicing
- Identify Candidate Genes
- Identify Differentially Expressed Gene Groups and Pathways
- Identify Highly Mutated Gene Groups and Pathways
- Identify Mutated Genes
- Select Genes by Name
- 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)
- Helper Tools
- Extract Sequences
- Filter Based on Overlap
- Cloning and Restriction Sites
- Add attB Sites (Gateway Cloning)
- Create Entry clone (BP) (Gateway Cloning)
- Create Expression clone (LR) (Gateway Cloning)
- Sanger Sequencing
- 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)
- Epigenomics Analysis
- Transcription Factor ChIP-Seq
- Annotate with Nearby Gene Information
The functionality of the CLC Server can be extended by installation of Server plugins. The available plugins can be found at http://www.qiagenbioinformatics.com/plugins/.