Oncoanalyser 3.0 for cancer genomics is out, now supporting Illumina, Ultima Genomics & Roche platforms

04-09-2026

Extensive work on the underlying WiGiTS tools now enable users to analyze sequencing data from three sequencing platforms (Illumina, Ultima Genomics & Roche) for comprehensive tumor characterization with a single, highly efficient and complete toolset.

A single integrated pipeline for clinical labs and researchers

The open-source cancer genomics WiGiTS toolset * developed by Hartwig Medical Foundation now supports data from three sequencing platforms: Illumina, Ultima Genomics and Roche Axelios. These changes have been packaged into a single integrative pipeline that is efficient and easy to run in release v3.0 of oncoanalyser**, co-developed by the Collaborative Centre for Genomic Cancer Medicine CCGCM in Melbourne. The extension means that clinical labs and researchers alike can run the same, thoroughly tested, analytical pipeline. Platform- and sample-specific error profiles and data structures are handled inside the pipeline and ensure that downstream results remain directly comparable across platforms.

Flexible study design: mix sequencing platforms within one workflow

Because platform support is decoupled from application, researchers and clinical laboratories can mix experimental designs within a single study or care pathway. A tumor biopsy can be sequenced on Illumina while matched circulating tumor DNA (ctDNA) monitoring or RNA profiling runs on Ultima Genomics or Roche, or vice versa, with all data converging on one interpretation layer. This opens opportunities to choose instruments as it is no longer tied to the analytical stack; this simplifies selection of technology and large-scale integration of data, including legacy cohorts.

Reduced vendor lock‑in and increased scientific freedom

We expect that having a user-friendly comprehensive analysis toolkit will lower the barrier for cancer research laboratories considering a change in sequencing vendor. When analysis pipelines are proprietary or tied to a single instrument, switching platforms means changing the entire bioinformatics toolset; with an open pipeline that is transparent and multi-platform, such migration costs are substantially reduced. This point is increasingly topical as laboratories are showing increased interest in these recently released sequencing technologies. By supporting 3 major vendors oncoanalyser enables decisions to be driven by scientific and operational merit rather than by lock-in.

* All Hartwig tools are freely available under the GPL-3.0 license

** oncoanalyser is freely available under the MIT license

Independent test data available via NIST HG008

Users that want to try the tools on independent data can check out the resources provided by the National Institute of Standard and Technology (NIST) for HG008, a cancer genome in a bottle.