DRAGEN ORA Helper Suite v2.0

Warning Do not use this documentation for decompression on the DRAGEN Server. The DRAGEN Server has its own integrated DRAGEN ORA Decompression component.

The DRAGEN ORA Helper Suite Software is a suite of software for Linux distributions, designed to integrate in a transparent manner compressed FASTQ.ORA files into secondary analysis in a local or remote environment.

In Illumina® DRAGEN™ Software v3.8 and later, the handling of FASTQ.ORA files is integrated within the system. DRAGEN ORA Helper Suite is intended for processing FASTQ.ORA files in environments where a secondary analysis is not performed on the DRAGEN Software or in environments that do not have access to DRAGEN v3.8 or later. If you are running secondary analysis pipelines on a DRAGEN v3.7 platform, only the oraFuse software is supported. Refer to oraFuse Software.

With the DRAGEN ORA Helper Suite, FASTQ.ORA files can be used:

• without full decompression to the disk

• with no overhead

• with no change in the current linux command (*.fastq is used instead of *.fastq.ora at input)

Software quick overview

The DRAGEN ORA Helper Suite Software package contains four software. Three of them process FASTQ.ORA files, the fourth one is an interactive user guide. You can use the FASTQ.ORA processing software in downstream analysis. The DRAGEN ORA Helper Suite Software v2.0 include:

• oraFuse v2.0

• ora-ldpreload v2.0

• orad v2.7.0

• oraHelper

oraFuse Software

The oraFuse software uses the FUSE filesystem to create a virtual ora subdirectory in the current directory, with ora symbolic links pointing to a virtual uncompressed FASTQ.ORA file. The virtual FASTQ file does not impact the storage footprint.

Info Root privileges are required to install the oraFuse software. If you do not have root privileges, use the ora LD-Preload software or the orad software.

ora LD-Preload Software

The ora LD-Preload software uses the LD-Preload variable of the dynamic linker to intercept stystem calls. The ora LD-Preload software creates a virtual FASTQ file for each FASTQ.ORA file. The virtual FASTQ files do not impact the storage footprint.

Info

• The ora LD-Preload software only works with a dynamically compiled binary. If you do not know if the intended downstream bioinformatics software has been dynamically compiled, run the oraHelper command for guidance.

• The auto-completion Linux feature does not work on virtual files.

orad Software

orad is the DRAGEN ORA Decompression software. Although it does not operate in a fully transparent manner, it works in most situations. The Orad software can be used in combination with the pipe process or pipe substitution process to reduce reads and writes to the disk.

oraHelper Interactive User Guide

oraHelper is an interective user guide that provides the following guidance:

• Which of the ORA Helper Suite software is the best fit.

• The proper command line to use with each of the ORA Helper Suite software.

• Information about the input file. For example, if a FASTQ.ORA file is a paired read interleaved file or which reference has been used to compress a FASTQ.ORA file.