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 | ||
Collapse Overlapping Annotations | ||
Convert DNA To RNA | X | |
Convert from Tracks | X | |
Convert RNA to DNA | X | |
Convert to Tracks | X | |
Copy Number Variant Detection (Targeted) | ||
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 Report from Table | ||
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 Genomes | ||
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 Track | X | |
Remove Marginal Variants | X | |
Remove Variants Present in Control Reads | X | |
Rename Sequences in Lists | ||
Resize Annotations | ||
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 |