Input Requirements

The pipeline accepts two 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.