genomics-pipeline

Step 1: ORA to FASTQ Conversion

What This Does

Converts Illumina’s proprietary ORA-compressed sequencing files into standard FASTQ format. ORA is Illumina’s lossless compression format (~3x smaller than gzip FASTQ).

Why

Raw sequencing data from Illumina DRAGEN comes in ORA format. All downstream tools expect FASTQ.

Tool

• orad (Illumina ORA decompression tool)
• Not available as Docker image — must be installed natively

Prerequisites

• orad binary (download from Illumina)
• Sufficient disk space: ORA→FASTQ expands ~3x (e.g., 30GB ORA → 90GB FASTQ)

Command

# Convert paired-end ORA files to FASTQ
orad --ora-reference /path/to/oradata/reference \
  sample_R1.ora sample_R2.ora \
  --output-directory /path/to/output/

# Output: sample_R1.fastq.gz, sample_R2.fastq.gz

Notes

• ORA reference files must match the sequencing run (provided alongside ORA files)
• If you receive FASTQ.gz directly (e.g., from a resequencing service), skip this step

This site is open source. Improve this page.