> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/ora/product-guides/dragen-ora-decompression/commands/with-downstream-analysis.md).

# 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](/ora/product-guides/dragen-ora-helper-suite.md) is recommended and available for download on the [ORA Support Site](https://support.illumina.com/sequencing/sequencing_software/DRAGENORA.html). 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.

{% hint style="info" %} <mark style="color:blue;">**Info**</mark>\
On Windows, replace `orad` with `orad.exe`\\
{% endhint %}


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