Combine with downstream analysis

For a fully transparent usage of fastq.ora files (no changes in the command, no overhead, no additional footprint) with third-party bioinformatics software, DRAGEN ORA Helper Suite Software is recommended and available for download on the ORA Support Site. This software is only supported on Linux.

For a semi-transparent usage of fastq.ora files with third-party bioinformatics software, use DRAGEN ORA Decompression with the pipe function or process substitution. This method improves system performance by reducing reads and writing to the disk versus a full decompression step.

• If the analysis software can read from the standard input, such as BWA, use the following command:

orad file.fastq.ora -c --raw | bwa mem humanref.fasta - > resu.sam

The -c option decompresses to standard output. The result is sent | to BWA, which uses the dash option - to read from standard input. This also works for paired reads, which uses the -p option of BWA to specify that the input contains interleaved paired reads.

• If the analysis software cannot read from the standard input, you can use process substitution:

bwa mem humanref.fasta <(orad file.fastq.ora -c --raw) > resu.sam

For the file name, use the <( ) syntax containing the command that generates the file to standard output. In this case, orad with the -c option as in the command above. This method does not work when the third-party software checks the input file name or when the third-party software does not read the file sequentially.

Info On Windows, replace orad with orad.exe