WiGiTS

WiGiTS is a universal open source suite of genome and transcriptome analysis tools for cancer research and diagnostics

The current release of the WiGiTs pipeline is v2.3. Release notes are here.

We recommend running WiGiTS with Oncoanalyser, a Nextflow implementation of the WiGiTS pipeline.

A detailed list of the resource files used to run the WiGiTs pipeline is here. Download links to the resource files can be found on the Oncoanalyser page.

The pipeline can be run on a targeted panel eg TSO500 - see detailed information here.

Pipeline overview

Here is a schematic showing how the interactions between the core molecular components of the tool suite:

Latest tool versions

Below are descriptions and download links for each tool used in the pipeline.

DNA Tools

| Component | Description | Current Version | |--------------------------------------------|------------------------------------------------------------------------|---------------------------------------------------------------------------------| | Amber | Generate a tumor BAF file for Purple's copy number fit | 4.2 | | BamTools | BAM metrics and slicing | 1.5 | | Chord | Homologous Recombination Deficiency detection | 2.2 | | Cider | TCR/BCR V(D)J recombination sequence detection | 1.1 | | Cobalt | Determines the read depth ratios for Purple's copy number fit | 2.2 | | Cuppa | Tissue of origin prediction from WGS/WTS | 2.4 | | Esvee | SV calling | 1.2 | | Lilac | HLA typing | 1.7 | | Linx | SV annotation, clustering & chaining, fusion and disruption calling | 2.2 | | Neo | Neoepitopes | 1.2 | | Pave | Point mutation annotation and gene impact | 1.8 | | Purple | Estimates copy number, purity and ploidy, and identifies driver events | 4.3 | | Redux | Duplicate marking, consensus reads, UMIs and read unmapping | 1.2 | | Sage | Point mutation variant calling and filtering | 4.2 | | Teal | Measures telomere content and estimates telomeric length | 1.3 | | Wisp | Measures purity in longitudinal samples | 1.2 |

The following external tools are also used in the pipeline:

| Component | Description | Current Version | |---------------------------------------------------------|-----------------------------------------------|-----------------------------------------------------------------------| | VirusBreakend | Viral integration detection | 2.13.2 |

RNA Tools

| Component | Description | Current Version | |------------------------------|------------------------------------------------------------|------------------------------------------------------------------------------| | Isofox | WTS Transcript Abundance, Fusions & Novel Splice Junctions | 1.7 |

Actionability and Clinical Reporting Tools

| 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 | 4.1 | | Patient-reporter | PDF summary report and JSON file of all clinical relevant WGS output | 7.25.1 |