Use of multi-core computers

Many tools in CLC Workbenches and Servers can make use of multi-core CPUs. This does not necessarily mean that all available CPU cores are used throughout the analysis. It means that these tools benefit from running on computers with multiple CPU cores.

Tools available differ between CLC Workbenches. In the table, the availability of these tools in different CLC Workbench Toolbox menus is indicated with an X.

 Use of multi-core computers Genomics Biomedical Genomics  
 Add Conservation Scores   X  
 Add Information about Amino Acid Changes   X  
 Add Information from Variants   X  
 Add Exon Number   X  
 Add Flanking Sequence   X  
 QC for Read Mapping   X  
 Amino Acid Changes X    
 Annotate and Merge Counts X X  
 Annotate from Known Variants X    
 Annotate with Conservation Score X    
 Annotate with Exon Numbers X    
 Annotate with Flanking Sequences X    
 Basic Variant Detection X X  
 BLAST (will not scale well on many cores) X    
 Compare Sample Variant Tracks X    
 Copy Number Variant Detection   X  
 Create Alignment X X  
 Create Detailed Mapping Report X    
 Create Sequencing QC Report X    
 Create Statistics for Target Regions X    
 De Novo Assembly X    
 Dock Ligands      
 Download Reference Genome Data X    
 Extract and Count X X  
 Filter against Control Reads X    
 Filter against Known Variants X    
 Filter Marginal Variant Calls X    
 Filter Reference Variants X    
 Fisher Exact Test X    
 Fixed Ploidy Variant Detection X X  
 GO Enrichment Analysis X    
 Identify Enriched Variants in Case vs Control Group   X  
 Identify Highly Mutated Gene Groups and Pathways   X  
 Identify Variants with Effect on Splicing   X  
 Import Molecules from SMILES or 2D      
 InDels and Structural Variants X X  
 K-mer Based Tree Construction X    
 Link Variants to 3D Protein Structure X X  
 Local Realignment X X  
 Low Frequency Variant Detection X X  
 Map Reads to Contigs X    
 Map Reads to Reference X X  
 Maximum Likelihood Phylogeny X    
 Merge Annotation Tracks X    
 Model Testing X    
 Predict Splice Site Effect X    

 Use of multi-core computers Genomics Biomedical Genomics  
 Probabilistic Variant Detection (legacy) X X  
 QC for Sequencing Reads   X  
 QC for Read Mapping   X  
 QC for Targeted Sequencing   X  
 Quality-based Variant Detection (legacy) X X  
 Remove False Positives   X  
 Remove Germline Variants   X  
 Remove Reference Variants   X  
 Remove Variants Found in Common dbSNP   X  
 Remove Variants Found in External Database   X  
 Remove Variants Found in HapMap   X  
 Remove Variants Found in 1000 Genomes Project   X  
 Remove Variants Inside Genome Regions   X  
 Remove Variants Not Found in External Database   X  
 Remove Variants Outside Genome Regions   X  
 Remove Variants Outside Targeted Regions   X  
 RNA-Seq Analysis X X  
 Screen Ligands      
 Trim Sequences X X  
 Trio Analysis X X  
Please note that a static license has a limitation on the maximum number of cores, see Limitations on maximum number of cores.