> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/tso500/dragen-tso-500-guides/dragen-tso-500-v2.5/analysis-methods.md).

# Analysis Methods

The software processes sequencing data to perform quality control, detect variants, determine tumor mutational burden (TMB), microsatellite instability (MSI) status, and genomic instability score (GIS), and report results. The following sections describe the analysis methods used in DRAGEN TruSight Oncology 500 Analysis Software.

DRAGEN TruSight Oncology 500 Analysis Software uses the following workflows to analyze sequencing data.

* FASTQ Generation
* DNA Analysis
  * DNA Alignment and Realignment
  * Read Collapsing
  * Small Variant Calling
  * Small Variant Filtering
  * Copy Number Variant (CNV) Calling
  * Phased Variant Calling
  * Variant Merging
  * Annotation
  * Tumor Mutational Burden (TMB) Scoring
  * Microsatellite Instability (MSI) Status
  * Contamination Detection
* RNA Analysis
  * Downsampling
  * Read Trimming
  * Alignment
  * Duplicate Marking
  * Fusion Calling
  * RNA Fusion Filtering
  * Splice Variant Calling
  * Annotation
  * Fusion Merging
* Quality Control
  * Run QC
  * DNA Sample QC
  * RNA Sample QC


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