Commands

Required commands

Use the following commands to decompress the files:

orad FILE [args]or orad [args] FILE

A folder that contains FASTQ.ORA files can also be provided for batch decompression of FASTQ.ORA files at top level directory:

orad ./pathtofolder/ [args]

On Windows, replace orad with orad.exe.

orad.exe FILE [args].

To decompress FASTQ.ORA compressed with a reference other than the default human reference, ensure the specific reference is available locally.

No change applies in the command line. The decompression software automatically detects which species/model is used.

Command Line Options

Command	Description
-C --check	Checks the integrity of the specified ORA file. This option decompresses the file in memory and verifies that the checksum of the decompressed data and the checksum of the original data are identical. The decompressed file is not saved.
--raw	Decompresses the ORA file into an uncompressed FASTQ file. By default, the DRAGEN ORA Decompression Software decompresses to gzip format.
--rm	Deletes the input file after successful execution. By default, the input file is not deleted. This option is not supported for files in AWS S3 or Azure Blob Storage.
-t --threads	Sets the maximum number of threads allowed by the system. The default value is 8.
-f --force	Overwrites the output file without prompting. By default, if the output file exists, the software exits without overwriting.
-h --help	Prints help and exits.
-v --version	Prints software version.
-i --info	Prints information about the compressed ORA file. The following information is included: Software version used to compress the file. Total number of sequences in the file. Total number of bases in the file. If the file contains interleaved data. The original name of the file if it was saved in the fastq.ora file. The name of the species/reference it has been compressed with, and the related xxhash checksum of the reference. When nothing is specified the FASTQ.ORA file has been compressed with the default human reference. This option is not supported for files in AWS S3 or Azure Blob Storage. Although the ORA file format supports concatenation of fastq.ora files, using this command on a concatenated fastq.ora file prints erroneous information.
-c --stdout	Prints the decompressed file to the default standard output stdout. This is useful to share the results with another application without writing the decompressed file to disk.
-	Reads an input fastq.ora file from the default standard input stdin. This option is not supported for Windows OS.
-P --path	Sets the path location of the output file. The default file name is used. If a path is not specified, the file is created in the same location as the input file.This option overwrites the path if it is used with the -o option.
-o --out	Sets the name of the output file and the path when used with -P. The default is the name of the input fastq.ora file.
-N --name	Restores the original name saved in the fastq.ora file, at the time it was compressed to a fastq.ora file.
-I --interleave	Decompresses the output file into a single interleaved file. By default, when the input is a single interleaved fastq.ora file, the decompression automatically decompresses into two separate paired read files. If the interleaved fastq.ora file was generated with DRAGEN ORA Decompression v.4.0 or later, -interleaved is included in the file name.
--ora-reference	Changes the directory of the ORA reference file refbin.By default the software looks for the reference file in the following locations: $HOME/oradata/refbin $HOME/oradata/Genus_specificname/refbin ./oradata/refbin ./oradata/Genus_specificname/refbin If you specified a location in the environment variable, the software also looks in the location ORA_REF_PATH. For example, set with export ORA_REF_PATH=/some/path/.
--check-ora-reference-path	Verifies if the ORA reference file refbin is accessible and prints the refbin path. Decompression does not occur when this option is added.
--quiet	Sets decompression to quiet mode. In quiet mode, nothing is written to the standard output and standard error. This mode is ignored when used with -c (--stdout) or -C (--check).
--empty-third-line	Outputs the third line in the FASTQ format, (which is, the line that starts with +) as an empty line. By default this line is preserved.
-r --repeat-header	Adds the read header to the third line in the FASTQ format, (which is, the line that starts with +).

Command Examples

Using Windows, replace orad with orad.exe. Example is: orad.exe myfile.fastq.ora --check

Command	Description
orad myfile.fastq.ora --check	Checks the integrity of an ora file.
orad myfile.fastq.ora	Decompresses myfile.fastq.ora to myfile.fastq.gz
orad myfile.fastq.ora --info	Prints information summary of an ora file.
orad -c --raw myfile.fastq.ora | head	Prints the first lines of the corresponding .FASTQ file in the terminal.
orad --check-ora-reference-path	Verifies the accessibility of the ora reference file and print its path.