# Commands for Interleaved fastq.ora files

If the input FASTQ.ORA file is an interleaved paired read file, it can be used as-is with downstream bioinformatics software which provide options to handle interleaved files. Make sure you are using the downstream bioinformatics software with proper interleaved options on the interleaved virtual FASTQ.

In the following example, after the oraFuse software has been mounted, the `bwa` command is used with the `–p` option to specify that the input contains interleaved paired reads.

`bwa mem reference.fasta -p <interleaved file>.fastq -o result.sam`

To decompress an interleaved FASTQ.ORA file into two separate files, use the orad software.

`orad <interleaved file>.fastq.ora`

To decompress into a single file with interleaved paired reads, use the `--interleave` option.

In the following example the orad software is used with the `bwa` command, and the `-–interleave` option is used to decompress into a single stream containing interleaved data.

`bwa mem reference.fasta -p <( orad -c --raw --interleave <interleaved file>.fastq.ora ) > result.sam`


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