> For the complete documentation index, see [llms.txt](https://help.connected.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.connected.illumina.com/run-set-up/overview/sample-sheet-structure.md). # Sample Sheet Structure The information contained within a sample sheet is organized into various sections, like Header, Reads, Manifests, Data, and Settings. There are two types of sections: **Standalone sections**—Contain run settings and data that do not pertain to a specific application. **Applications sections**—Contain run settings and data required by specific applications. ### Standalone Sections The Header and Reads sections contain run settings and data. The Header and Reads sections are present in every v2 sample sheet. Additional standalone sections such as Sequencing Settings can be added and do not produce an error. A new section includes a section header that precedes the data contained within the section. A section header consists of the name of the section within brackets, as seen in the first line of the following example. ``` [Header],,, FileFormatVersion,2,, RunName,MyRun,, InstrumentPlatform,NextSeq1k2k,, InstrumentType,NextSeq2000,, ,,, ``` ### Application Sections The application sections contain data required to run Illumina applications. Application settings differ from instrument to instrument. Refer to the applicable[ instrument settings](/run-set-up/overview/instrument-settings.md) section. Designate an applications section by appending Settings or Data to the section name as seen in the following example. ``` ,,, [BCLConvert_Settings],,, SoftwareVersion,x.y.z,, ,,, ,,, [BCLConvert_Data],,, Lane,Sample_ID,index,index2 1,S01-TOO-12plex-P1-rep1,ATCCACTG,AGGTGCGT 1,S02-TOO-12plex-P1-rep2,GCTTGTCA,GAACATAC 1,S03-TOO-12plex-P1-rep3,GCTTGTCA,GAACATAC 1,S04-TOO-12plex-P1-rep4,GCTTGTCA,GAACATAC ``` Each application can have a maximum of one Settings section and one Data section. **Settings section**—This section contains key-value pairs that configure settings for the application, as seen in the example. The Settings section is applied globally to all samples. **Data section**—This section contains per sample data (in tabular format) used as input by the given application. The data in the first non-empty line of the application data section forms the column headers for the rest of the section. The Data section is uniquely applied to each sample. --- # 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.connected.illumina.com/run-set-up/overview/sample-sheet-structure.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.