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
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