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 implementation called OncoAnalyser.
The pipeline can be run on a targeted panel eg TSO500 - see detailed information here.
Here is a schematic showing how the interactions between the core molecular components of the tool suite:
The next planned release of the WiGiTs pipeline is v2.0, expected to be available on nfCore during April. Release notes are here:
The table below has links for 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 |
| Chord | Homologous Recombination Deficiency detection | 2.0 |
| 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 | 1.1 |
| Sage | Point mutation variant calling and filtering | 4.0 |
| Teal | Measures telomere content and estimates telomeric length | 1.3 |
The following external tools are also used in the pipeline:
| Component | Description | Current Version |
|---|---|---|
| VirusBreakend | Viral integration detection | 2.13.2 |
| 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 | 3.7.1 |
| 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.
