# 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 * Indel realignment and read stitching * 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 --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://help.tso500software.illumina.com/dragen-tso-500-ctdna-guides/dragen-tso-500-ctdna-v2.6/analysis-methods.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.