Operational Modes

STRmie-HD provides two main CLI modes: Complete_Pipeline and Index_Calculation.

Complete Pipeline

This mode executes the entire workflow starting directly from raw sequencing data (.fastq.gz or .fasta.gz).
It automatically performs:

Histogram-based CAG allele peak calling.
CCG repeat assignment for each allele.
Calculation of Instability and Expansion indices (II, EI).
Detection of Loss of Interruption (LOI) and Duplication of Interruption (DOI) events.
Generation of both an Excel summary report and an interactive HTML report for visual inspection.

Optional graphical outputs (CAG/CCG histograms) and raw read-level counts are also produced for each sample if requested.

Index Calculation

This mode is intended for situations where automatic allele calling requires manual adjustment.
When inspecting the interactive HTML report, the user may decide that the automatically identified allele peaks are not accurate.
Through the HTML interface, it is possible to:

Visually explore CAG and CCG histograms for each sample.
Manually adjust allele peak values if necessary.
Export a curated Excel table with the corrected allele definitions.

The Index_Calculation mode takes this adjusted table as input and recomputes all instability and expansion indices (II, EI) accordingly.
This ensures that downstream results are based on manually validated allele assignments.