WiGiTS is a universal open source suite of genome and transcriptome analysis tools for cancer research and diagnostics
We recommend to run WiGiTS using the NextFlow implmentation called OncoAnalyser.
Alternatively, an example WGS pipeline which runs each of these components in turn is detailed here.
An example targeted-panel pipeline, including support for the HMF and TSO-500 panels, is detailed here.
Here is a schematic showing how the interactions between the core molecular components of the tool suite:
The latest HMF pipeline is v6.0. Release notes are here.
The table below has links for the each tool used in this release.
| Component | Description | Current Version |
|---|---|---|
| Amber | Generate a tumor BAF file for Purple's copy number fit | 4.1 |
| BamTools | BAM metrics and slicing | 1.3 |
| Cider | TCR/BCR V(D)J recombination sequence detection | 1.0.3 |
| Cobalt | Determines the read depth ratios for Purple's copy number fit | 2.0 |
| Cuppa | Tissue of origin prediction from WGS/WTS | 2.3 |
| Esvee | SV calling | 1.0 |
| Lilac | HLA typing | 1.6 |
| Linx | SV annotation, clustering & chaining, fusion and disruption calling | 2.0 |
| Pave | Point mutation annotation and gene impact | 1.7 |
| Purple | Estimates copy number, purity and ploidy, and identifies driver events | 4.1 |
| Redux | Duplicate marking, consensus reads, UMIs and read unmapping | 1.0 |
| Sage | Point mutation variant calling and filtering | 4.0 |
| Teal | Measures telomere content and estimates telomeric length | 1.3.0 |
The following external tools are also used in the pipeline:
| Component | Description | Current Version |
|---|---|---|
| VirusBreakend | Viral integration detection | 2.13.2 |
| Chord | Homologous Recombination Deficiency detection | 2.0 |
| Component | Description | Current Version |
|---|---|---|
| Isofox | WTS Transcript Abundance, Fusions & Novel Splice Junctions | 1.7 |
| Component | Description | Current Version |
|---|---|---|
| Protect | Matching of molecular results to treatments and clinical trials | 2.3 |
| Rose | Actionability of clinically relevant molecular findings | 1.3 |
| Virus Interpreter | Filtering, annotation and interpretation of virus breakend data | 1.3 |
| Orange | PDF summary report and JSON file of all WGS output | 3.5.0 |
| Patient-reporter | PDF summary report and JSON file of all clinical relevant WGS output | 7.25.1 |
Resource files for each component (GRCh37 and GRCh38) are available to download from HMFTools-Resources > DNA-Resources.