# Input Requirements

The pipeline accepts these types of input data.

## Illumina Reads
*   **Format**: Paired-end FASTQ files (`.fastq.gz`).
*   **Naming**: `*_1_illumina.fastq.gz` and `*_2_illumina.fastq.gz`.

## Nanopore Reads
*   **Format**: Single-end FASTQ files (`.fastq.gz`).
*   **Naming**: `*_ont.fastq.gz`.

## Raw VCFs
*   **Format**: VCF files (`.vcf` or `.vcf.gz`).