Mapping Sequencing Runs to Biosamples

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.

Sample SheetBiosample DataDescription

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.


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.


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



  • 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.

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.

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