Sample Sheet

What is a Sample Sheet?

A sample sheet is a comma-separated value (*.csv) file format used by Illumina instruments, platforms, and analysis pipelines to store settings and data for sequencing and analysis. The sample sheet uses American Standard Code for Information Interchange (ASCII) character encoding.

The system using the sample sheet as input validates the data within the sample sheet based on validation rules. Validation rules differ from section to section. Incorrectly formatted data are considered invalid and causes software to throw an error. Refer to the validation rules for each section for more information on acceptable formatting and allowable values.

How to Use a Sample Sheet?

A v2 sample sheet can be obtained from one of the following options.

1. A v2 sample sheet can be created in BaseSpace using Run Planning.

   1. In BaseSpace Sequence Hub, select the Runs tab > New Run > Run Planning > Local Mode > Export Sample Sheet.

   2. For this option, all sample and index information is entered in Run Planning and is included in the exported v2 sample sheet.

2. A v2 sample sheet template can be downloaded and filled out manually.

   1. Download the template with the link below and use a text editor program to alter the sections according to your chosen instrument or analysis. Using a spreadsheet editor can cause errors with sample sheet validation and analysis. Save the sample sheet to a folder accessible by your instrument or analysis software.

   2. Follow instructions to fill out the sample sheet. See resources below:

      1. Sample Sheet Structure

      2. Instrument Settings

      3. Cloud Analysis Auto-launch Settings

      4. Index Orientation Guide

      5. Resources

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SampleSheet_v2_template.csv