XOOS analysis tools
XOOS analysis tools are hosted by Roche on Github
Enabling the future of NGS with SBX-optimized integrated and standalone analysis tools
The AXELIOS 1 Platform is set to shape the future of NGS with the speed, accuracy, scalability and flexibility it offers. With the advent of this novel technology comes the need for analysis tools equipped to maximize its value. To do this, the platform combines the speed and flexibility of integrated analysis workflows with the customizability and performance of standalone XOOS analysis tools. This comprehensive approach delivers the acceleration and versatility needed to transform high-throughput sequencing data into biological insights.
Integrated analysis
AXELIOS 1 integrated analysis workflows accelerate the path to discovery by analyzing data where it’s generated, as it’s generated. These workflows combine high-performance compute with real-time sequencing data processing, spanning base calling to mapped and aligned reads** while the run is underway.1 As a result, the AXELIOS 1 Platform offers exceptionally rapid turnaround times for multiple data outputs in standard file formats.
Flexible data off-ramps for diverse research needs
View full tableFlexible data off-ramps for diverse research needs
AXELIOS 1 Platform offers multiple data off-ramps within the workflow to provide maximum flexibility in meeting a diverse set of sequencing workflow and application development needs.
AXELIOS 1 Platform offers multiple data off-ramps within the workflow to provide maximum flexibility in meeting a diverse set of sequencing workflow and application development needs.
| Data Output Type | Supported SBX-Workflows | Output Format | Characteristics | Data Footprint§ (16-plex, 4 hour SBX-D Run) |
Analysis Turnaround Time†,‖ |
| Raw Reads | SBX-D, SBX-S | fastq.gz‡ (non-demultiplexed) |
|
~ 2.3 - 2.6 TB | ~6.5 - 11 hrs |
| Consensus Reads | SBX-D | fastq.gz‡ (sample-specific) |
|
~ 1.1 - 1.3 TB | ~5 - 6.5 hrs |
| Mapped/Aligned reads | SBX-D | BAM (sample-specific, indexed) |
|
~ 1.1 - 1.5 TB | ~5.5 hrs |
†Turnaround times are approximate and based on runs consisting of a 4 hour sequencing time and 16 SBX-D human whole genome samples, and include transfer times observed when using a dedicated 10 Gbps line and transferring to local storage.
‡fastq files generated using gzip compression with a compression setting of 6.
§File size ranges are estimates of run-level sizes for runs using a 4 hour sequencing time and 16 SBX-D human whole genome samples.
‖Analysis times and file sizes provided are approximate and should be used as guidance. Observed analysis times and file sizes are dependent on a number of experimental factors and may vary.
Standalone XOOS analysis tools
The speed, flexibility, and efficiency of AXELIOS 1 Platform integrated compute is complemented by our suite of customizable, SBX-optimized, XOOS (pronounced “zoose”) analysis tools. Hosted on Github and capable of being deployed on local or cloud compute infrastructure, these high-performing, scalable tools provide foundational data analysis building blocks for creating robust data pipelines and enabling the SBX analysis ecosystem for a diverse range of applications and variant types.
Access the data set
Create your account to access the whole genome sequencing SBX-D genome in a bottle (GIAB) data set.2
AXELIOS 1 data analysis resources
Analysis tool documentation
Supporting documentation for XOOS analysis tools is hosted by Roche on Gitbook
Download our white paper
Germline variant calling using SBX with DeepVariant
Explore how SBX, when coupled with advanced bioinformatics tools like a pangenome aligner and DeepVariant, provides accurate germline variant identification from whole-genome sequencing (WGS) data.
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Explore articles from our community
* For Research Use Only. Not for use in diagnostic procedures. AXELIOS is a trademark of Roche.
** Real-time refers to the ability to process data from an ongoing sequencing run in parallel with said sequencing run.
Lag time between sequencing run completion and analysis completion is expected for both fastq.gz and bam outputs.
Ability to perform demultiplexing, intramolecular consensus and or mapping/alignment in real-time currently pertains to only SBX-D workflows.
Conversion to fastq.gz occurs in real-time.
References:
- Roche Diagnostics & GenomeWeb. Germline Small Variant Calling Workflow for SBX Duplex Data [Internet; cited 2026 Jun 15]. Available from: https://diagnostics.roche.com/us/en/article-listing/diagnostics-insights/sequencing-by-expansion-duplex-sbx-d-data-analysis.html
- Zook J, et al. Extensive sequencing of seven human genomes to characterize benchmark reference materials. Sci Data. 2015;3:160025.