> 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-helper-suite/interleaved-files.md). # 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 .fastq -o result.sam` To decompress an interleaved FASTQ.ORA file into two separate files, use the orad software. `orad .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 .fastq.ora ) > result.sam` --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation by asking a question. Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters: ``` GET https://help.bioinsight.illumina.com/ora/product-guides/dragen-ora-helper-suite/interleaved-files.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.