The sample sheet is a comma-delimited file (SampleSheet.csv) that stores the information needed to set up and analyze a sequencing experiment. The file includes a list of samples, their index sequences, and the sequencing workflow.
Every run in BaseSpace Sequence Hub requires an associated sample sheet to define projects and samples, assign indexes, and run workflow apps.
Use Illumina Experiment Manager software to set up a sample sheet for your library prep protocol.
BaseSpace Sequence Hub maps sample sheet data to biosamples and libraries in your account. To make sure the data in your sample sheet are associated correctly, upload your biosamples before you upload the sample sheet. For more information, see .
Data from sample sheets are matched to existing biosamples, libraries, and pools in the account belonging to the run owner. If the data do not match exactly, the biosamples, libraries, or pools are added as new. To correct mismatch errors, fix the sample sheet and perform a run requeue. For more information about fixing sample sheets, see Fix Sample Sheet.
To ensure that run data is correctly matched to entities in BaseSpace Sequence Hub, upload biosamples using a biosample workflow file, CLI, or API before uploading the sample sheet. For more information about uploading biosamples, see Biosample Workflow.
The following table lists the sample sheet data that is matched to biosample data.
In the following example, the sample name is missing. BaseSpace Sequence Hub creates a new library using the Saliva 2 name from the provided sample ID.
Sample ID
Biosample Name
If the Sample ID does not exactly match the name of a biosample associated with the specified default project in the run owner's account, BaseSpace Sequence Hub creates a new biosample from the Sample ID and associates incoming FASTQ data with the new biosample.
If the Sample ID matches a biosample name in the run owner's account, its data are aggregated to the existing biosample name.
For MiSeq instruments running Targeted RNA or Amplicon DS, the biosample name is created from the sample sheet as SampleName-SampleID, and the library name is set to default.
Project
Default Project
Sample Name
Library name
If the library is not already associated with the biosample, BaseSpace Sequence Hub creates a new library using the sample name.
If the sample name is not defined in the sample sheet, BaseSpace Sequence Hub creates a library name with the same name as the sample ID.
n/a
Library Prep Kit
If the biosample exists and has an active Prep Request, the Library Prep Kit from the Prep Request is used. If there is no Prep Request, the Library Prep Kit is set to Unknown.
Sample Plate
Container name
Sample Well
Container Position
Lanes
Pool
New pools are created for each lane with more than one library. If the same libraries (same names and indexes) are present in more than one lane of a run, a single pool is created and associated with each lane. However, if a lane has libraries that match a pool from a prior run, a new pool is created.
If there is no Lane data, all libraries are combined into a single pool.
One pool is created for each unique group in the lane column.