> 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-ctdna-guides/dragen-tso-500-ctdna-v2.6/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 report results. The following sections describe the analysis methods used in DRAGEN TruSight Oncology 500 ctDNA Analysis Software.

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

* FASTQ Generation
* DNA Analysis
  * Contamination Detection
  * Copy Number Variant (CNV) Calling
  * DNA Alignment and Read Collapsing
  * Fusion Calling
  * Fusion Filtering
  * Max Somatic AF
  * Microsatellite Instability (MSI) Status
  * Phased Variant Calling
  * Small Variant Calling
  * Small Variant Filtering
  * Tumor Mutational Burden (TMB) Scoring
  * Variant Merging
* Quality Control
  * Run QC
  * DNA Sample QC


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