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 section.

Designate an applications section by appending Settings or Data to the section name as seen in the following example.

<Enter analysis settings for demultiplexing. Used by BCL Convert software.>,,,
[BCLConvert_Settings],,,
SoftwareVersion,x.y.z,,
,,,
<Enter sample information of each sample in the run for demultiplexing. Used by BCL Convert software.>,,,
[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.