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