Non-exclusive Algorithms
Tools categorized as non-exclusive or streaming are listed in table below. Non-exclusive jobs have low resource demands and can be run concurrently on an execution node. Streaming jobs are I/O intensive. On single servers or job nodes, these can be run alongside non-exclusive tools, but not alongside other streaming tools on a given execution node. Exclusive tools always run alone. On grid nodes, streaming tools are treated as exclusive, and thus are always run alone.
Documentation about configuring simultaneous job execution:
- For job nodes, see Configuring your job node setup.
- For grid setups, see Multi-job processing on grid.
- For single servers, see Single Server setup.
| Tool | Streaming | |
| Add attB Sites | ||
| Amino Acid Changes | X | |
| Annotate from Known Variants | X | |
| Annotate with Conservation Scores | X | |
| Annotate with Exon Numbers | X | |
| Annotate with Flanking Sequences | X | |
| Annotate with Nearby Gene Information | ||
| Annotate with Overlap Information | X | |
| Annotate with Repeat and Homopolymer Information | ||
| Apply Peak Shape Filter | ||
| Assemble Sequences | ||
| Assemble Sequences to Reference | ||
| BLAST at NCBI | ||
| Call Methylation Levels | ||
| ChIP-Seq Analysis | ||
| Convert DNA To RNA | X | |
| Convert from Tracks | X | |
| Convert RNA to DNA | X | |
| Convert to Tracks | X | |
| Copy Number Variant Detection (CNVs) | ||
| Count-based statistical analysis | ||
| Create Alignment | ||
| Create BLAST Database | ||
| Create Box Plot | ||
| Create Entry Clone (BP) | ||
| Create Expression Browser | ||
| Create Expression Clone (LR) | ||
| Create GC Content Graph Track | ||
| Create Histogram | ||
| Create K-medoids Clustering for RNA-Seq | ||
| Create MA Plot | ||
| Create Mapping Graph Track | ||
| Create RRBS-fragment Track | ||
| Create Sample Report | ||
| Create Sequence Statistics | ||
| Create Track from Experiment | ||
| Create Track List | ||
| Create Tree | ||
| Create Venn Diagram for RNA-Seq | ||
| Demultiplex Reads | ||
| Download 3D Protein Structure Database | X | |
| Download BLAST Databases | X | |
| Download Pfam Database | X | |
| Extract Annotations | ||
| Extract Consensus Sequence | ||
| Extract IsomiR Counts | ||
| Extract Reads | ||
| Extract Sequences | X | |
| Filter against Known Variants | X | |
| Filter Annotations on Name | X | |
| Filter Based on Overlap | X | |
| Find and Model Structure | X | |
| Find Binding Sites and Create Fragments | ||
| Find Open Reading Frames | ||
| Gaussian Statistical Analysis | ||
| Gene Set Test | ||
| GO Enrichment Analysis | ||
| Hierarchical Clustering of Samples | ||
| High-throughput sequencing importers (e.g. Illumina) | X | |
| Identify Enriched Variants in Case vs Control Samples | X | |
| Identify Graph Threshold Areas | ||
| Identify Known Mutations from Mappings | ||
| Import Primer Pairs | ||
| Import SAM/BAM/CRAM Mapping Files | X | |
| Import Tracks from File | ||
| InDels and Structural Variants | ||
| Learn Peak Shape Filter | ||
| Link Variants to 3D Protein Structure | X | |
| Merge Annotation Tracks | X | |
| Merge Overlapping Pairs | ||
| Merge Read Mappings | X | |
| Merge Variant Tracks | ||
| Motif Search | ||
| Pfam Domain Search | X | |
| Predict Splice Site Effect | ||
| Principal Component Analysis | ||
| Probabilistic Variant Detection | ||
| Proportion-based Statistical Analysis | ||
| Quality-based Variant Detection | ||
| Quantify miRNA | ||
| QC for Read Mapping | ||
| QC for Sequencing Reads | X | |
| QC for Targeted Sequencing | ||
| Remove Duplicate Mapped Reads | ||
| Remove Homozygous Reference Variants | ||
| Remove Information from Variants | X | |
| Remove Marginal Variants | X | |
| Remove Variants Present in Control Reads | X | |
| Rename Sequences in Lists | ||
| Reverse Complement Sequence | ||
| Subsample Sequence List | ||
| Secondary Peak Calling | ||
| Score Regions | ||
| Split Sequence List | ||
| Transcription Factor ChIP-Seq | ||
| Translate to Protein | ||
| Trim Sequences | ||
| TRIO analysis | ||
| Update Sequence Attributes in Lists | ||
| Whole Genome Coverage Analysis |