# STRmie-HD Documentation

**STRmie-HD** (Short Tandem Repeat Mapping and Identification Engine – Huntington's Disease) is an interactive, Python-based tool designed to support the curation, visualization, and interpretation of short tandem repeat (STR) genotyping data obtained from Huntington's Disease (HD) patients. It enables the prediction, refinement and validation of CAG/CCG repeat expansion results in the context of HD, by highlighting cases of allelic instability or potential misclassification.

```{toctree}
:maxdepth: 2
:hidden:

installation
input-file-types
operational-modes
usage
case-study
outputs
faq
```

## Overview
- Analysis and curation of STR Huntington's Disease genotypes (CAG/CCG)
- Calculation of Instability Index (II) and Expansion Index (EI)
- Local graphical interface for manual inspection (HTML report)

## Useful Links
- Source code: https://github.com/mazzalab/STRmie-HD
- License: MIT