Genomic Data Compression

Enancio is a company recently acquired by Illumina with proprietary lossless data compression technology specifically designed for genomics data. The software company, based in Cesson-Sévigné, France, joins a suite of exceptional bioinformatics offerings, with the goal of making genomics data processing, storage, and transfer more efficient and user-friendly.

ORA compression technology is being integrated across the Illumina portfolio in stages and will give users the option to produce compressed FASTQ files that are up to 5x smaller than fastq.gz¹. Compression is already available on the NextSeq 1000 and NextSeq 2000 Systems and NovaSeq X Series. Starting with the v3.8 release, compression is also available on DRAGEN servers with native ingestion of compressed FASTQ files into the DRAGEN mapper.

During the NGS workflow, you can optionally enable compression to generate compressed fastq.ora files. With the DRAGEN v3.8 release, fastq.ora files can be directly ingested by the DRAGEN mapper for a seamless integration. In addition, fastq.ora files can be decompressed on-the-fly for other mapping and downstream analyses. The integration of compression within DRAGEN BCL conversion streamlines the workflow, as shown in the figure below:

ORA compression technology used within DRAGEN

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Before acquisition of Enancio: compression as a standalone software. Compression is an extra step.

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The output of ORA compression technology is a compressed FASTQ binary file format: fastq.ora. This file format can be stored and shared to enable significant storage cost savings and reduced file transfer times. All compressed files can be decompressed with the freely available decompression software.

Fastq.ora files can be decompressed on the fly for mapping and downstream analysis or directly ingested by DRAGEN.

A 235 GB raw FASTQ file can be compressed to 55 GB via gzip. The data footprint is further reduced to 11 GB with DRAGEN ORA compression technology².

FASTQ files and BAM or CRAM files are typically stored for different purposes. However, fastq.ora files enable you to store a compressed copy of your raw data with a preserved MD5 sum and smaller footprint than the corresponding CRAM file.

DRAGEN can now enable compression of two different formats: FASTQs and BAMs to fastq.ora and CRAM, respectively.

Utilization of the compression is completely optional. DRAGEN users remain free to adopt the storage strategy they want: activate the conversion to Illumina FASTQ compressed file format and store these files, disable the conversion to DRAGEN ORA compressed file format fastq.ora and store fastq.gz, or store BAM or CRAM files.

With the DRAGEN 3.8 release, data compression is seamless and compressed fastq.ora files are directly ingested into the DRAGEN mapper.

Additionally, once the free decompression software is installed, a simple command can be used to directly pipe the output of decompression on the fly into a wide range of popular mapping tools such as BWA³, STAR⁴, and Bowtie⁵.

DRAGEN ORA FASTQ compressed files can be shared. The decompression software is freely available. Once the free decompression software is installed, a simple command can be used to directly pipe the output of decompression on the fly into a wide range of popular mapping tools such as BWA³, STAR⁴, and Bowtie⁵.