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).