Use of multi-core computers
The tools listed below can make use of multi-core CPUs. This does not necessarily mean that all available CPU cores are used throughout the analysis, but that these tools benefit from running on computers with multiple CPU cores.
- Amino Acid Changes
- Annotate from Known Variants
- Annotate with Conservation Scores
- Annotate with Exon Numbers
- Annotate with Flanking Sequences
- Basic Variant Detection
- BLAST (will not scale well on many cores)
- Call Methylation Levels
- Copy Number Variant Detection
- Create Alignment
- Create RRBS-fragment Track
- Demultiplex Reads
- De Novo Assembly
- Differential Expression
- Differential Expression in Two Groups
- Filter against Known Variants
- Filter based on Overlap
- Fixed Ploidy Variant Detection
- GO Enrichment Analysis
- Identify Enriched Variants in Case vs Control Samples
- InDels and Structural Variants
- K-mer Based Tree Construction
- Link Variants to 3D Protein Structure
- Local Realignment
- Low Frequency Variant Detection
- Map Bisulfite Reads to Reference
- Map Reads to Contigs
- Map Reads to Reference
- Maximum Likelihood Phylogeny
- Merge Annotation Tracks
- Merge Variant Tracks
- Model Testing
- Predict Splice Site Effect
- QC for Read Mapping
- QC for Sequencing Reads
- QC for Targeted Sequencing
- Remove Variants Present in Control Reads
- Remove Marginal Variants
- RNA-Seq Analysis
- Trim Reads
- Trio Analysis