DRAGEN ORA Compression and Decompression

The following example command contains the required DRAGEN ORA compression options.

or

The following example command contains the required ORA decompression options.

The following examples command contains the required options to compress FASTQs of a fastq-list.csv file containing multiple samples.

When all samples must be compressed:

When only specific samples must be compressed:

The following examples command contains the required options to achieve an interleaved compression of paired-read files from a fastq-list.csv file :

The following example command prints the file information summary of an ORA compressed file. Compression or decompression is not performed.

The following example command compares FASTQ file checksum and decompressed FASTQ.ORA file checksum and outputs ORA integrity check successful if both checksums are equal or integrity check failed if checksums are not equal.

The following are the command line options for running DRAGEN ORA compression and decompression.

Option	Required	Description
--enable-map-align	Yes	Set to false.
--enable-ora	Yes	Set to true to enable FASTQ file compression and decompression. Decompression must be enabled using the --ora-decompress option.
--ora-reference	Yes	Path to the directory that contains the compression reference and index file.
--ora-input	Yes (or --fastq-list)	Specify the input files for compression or decompression.
--fastq-list	Yes (or --ora-input)	Specify a .csv file with list of FASTQ files to be compressed. This option is not specific to the DRAGEN ora compression and the usage is explained in the FASTQ CSV File Format Section of this manual.
--ora-input2	No	Specify a second list of files to perform paired compression. The number of files should be the same as --ora-input.   Used for interleaved compression of paired-read files when input files are specified with --ora-input. Specify the paired-read files corresponding to files secified in --ora-input to achieve paired-read file compression into one single interleaved file. The number of files and the order of paired-read files in --ora-input and --ora-input2 should match.
--ora-interleaved-compression	No	Used for interleaved compression of paired-read files when input files are specified with --fastq-list. Set to true to enable paired-read file compression into one single interleaved file. Each line of the fastq-list.csv file is the two corresponding paired-read files with same count of reads.
--ora-decompress	No	Set to true to enable decompress mode. The default value is false.
--force	No	Compress to output directory even if the compressed file already exists. The existing compressed file is overwritten.
--ora-threads-per-file <#>-	No	Manually control the number of CPU threads for compressing each FASTQ input file. The default value is 8.
--ora-parallel-files <#>	No	Manually control the number of input FASTQ files processed in parallel. The default value is 4.
--ora-use-hw	No	Set to true to enable hardware acceleration or to false to disable hardware acceleration. The default value is true.
--ora-print-file-info	No	Print file information summary of ORA compressed files. This option cannot be used simultaneously with the ora-decompress and --ora-check-file-integrity options.
--ora-check-file-integrity	No	Set to true to perform and output result of FASTQ file and decompressed FASTQ.ORA integrity check. The default value is false. This option cannot be performed in the same command line than the compression itself as it requires fastq.ora format for the --ora-input argument.,
--ora-enable-md5	No	Set to true to compute md5 checksum of fastq.ora files during the compression and generate an ora.md5sum file with md5 checksum printed.
--ora-delete-input-files	No	Set to true to automatically delete the input FASTQ file from the disk upon completion of compression

Use the --output-directory option to specify the directory to store output compressed/decompressed files.

There are two methods to achieve a paired compression:

•

when using --ora-input and --ora-input2. The nth file of the --ora-input list is compressed together with the nth file of the --ora-input2

•

when using --fastq-list and --ora-interleaved-compression set to true. The paired-read files from the nth line of fast-list.csv are compressed together

Both files are interleaved within a single ORA output file with file name being <longest common uninterrupted name between the R1 filename and the R2 filename>-interleaved.fastq.ora. You can use these options to compress paired files together, which improves compression by up to 10%. If decompressing an ORA file that contains paired data, the file is automatically decompressed to two separate files. To map an ORA file that contains paired interleaved data with the DRAGEN mapper, use the --interleaved option.

To compress or decompress ORA files, you must provide an ORA reference file and specify an ORA reference directory. You can download ORA reference files from the Illumina DRAGEN Bio-IT Platform Product Files support page.

To specify an ORA reference directory, do as follows.

1.

Download the oradata-2.tar.gz file from the Illumina DRAGEN Bio-IT Platform Support Site.

2.

Move the file to the location you would like to contain the reference directory in, and then enter the following to extract the contents.

tar -xzvf oradata-2.tar.gz

3.

Set the --ora-reference command line option to the extracted /oradata folder path.

To use FPGA acceleration for DRAGEN ORA compression and DRAGEN ORA decompression, set --ora-use-hw to true. If you set --ora-use-hw to false, you can launch DRAGEN ORA compression/decompression in parallel to other processes that use FPGA when using on-site systems. Execution of DRAGEN ORA compression or decompression, in parallel with DRAGEN analysis, is not supported on the cloud.