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  1. Product Guides
  2. DRAGEN ORA Decompression v2.7
  3. Commands

Combine with downstream analysis

PreviousCommandsNextCheck Losslessness

Last updated 10 months ago

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For a fully transparent usage of fastq.ora files (no changes in the command, no overhead, no additional footprint) with third-party bioinformatics software, is recommended and available for download on the . 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

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