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Various algorithms for analysing genomics data

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WiGiTS

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

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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.

Pipeline overview

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

Latest Pipeline Version

The latest HMF pipeline is v5.34. Release notes are here.

The table below has links for the each tool used in this release.

DNA Tools

Component Description Current Version
Amber Generate a tumor BAF file for Purple's copy number fit 4.0.1
BamTools BAM metrics and slicing 1.2
Cider TCR/BCR V(D)J recombination sequence detection 1.0.3
Cobalt Determines the read depth ratios for Purple's copy number fit 1.16
Cuppa Tissue of origin prediction from WGS/WTS 2.1.1
Gripss SV filtering 2.4
Lilac HLA typing 1.6
Linx SV annotation, clustering & chaining, fusion and disruption calling 1.25
Pave Point mutation annotation and gene impact 1.6
Purple Estimates copy number, purity and ploidy, and identifies driver events 4.0
Redux Duplicate marking, consensus reads, UMIs and read unmapping 1.1.7
Sage Point mutation variant calling and filtering 3.4
Teal Measures telomere content and estimates telomeric length 1.3.0
SvPrep Pre-GRIDSS BAM filtering 1.2.3

The following external tools are also used in the pipeline:

Component Description Current Version
GRIDSS Structural variant calling 2.13.2
Chord Homologous Recombination Deficiency detection 2.0

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 3.5.0
Patient-reporter PDF summary report and JSON file of all clinical relevant WGS output 7.25.1

Resource files

Resource files for each component (GRCh37 and GRCh38) are available to download from HMFTools-Resources > DNA-Resources.

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