Automation Overview/Automatic Data Flow

Automatic Data Flow

The following diagram illustrates the data flow and automation steps in BaseSpace Sequence Hub.

  1. Biosample Workflow File Imported—Biosamples, library prep instructions, and analysis workflow instructions are uploaded via a Biosample Workflow file. BaseSpace Sequence Hub creates new biosamples and schedules analyses.
    After validating the manifest, BaseSpace Sequence Hub creates a new biosample and associated library prep requirements, and schedules a new analysis which includes Analysis QC thresholds and a yield dependency.
  2. Library Prep—Library prep status and QC are updated in BaseSpace Sequence Hub.
  3. Automatic Lane QCBaseSpace Sequence Hub automatically performs Lane QC on the new sequencing data based on the configured lane QC thresholds.
  4. Streaming Sequencing Data—The lab loads a flow cell and starts sequencing. Sequencing data begins to arrive in BaseSpace Sequence Hub.
  5. Automatic FASTQ Dataset GenerationBaseSpace Sequence Hub performs demultiplexing, if needed, and generates FASTQ data sets for each library by lane and index (if indexing). QC passed files are added to the yield calculations for the biosample.
  6. Automatic App LaunchBaseSpace Sequence Hub automatically launches pending analyses that have yield dependencies met with the new data.
    BaseSpace Sequence Hub aggregates all FASTQ data sets for a biosample as inputs to the analysis, excluding those that are QC Failed. Datasets can originate from multiple flow cells or other uploads.
  7. Automatic Analysis QCBaseSpace Sequence Hub automatically performs analysis QC after analyses complete.
  8. Mark Analyses for DeliveryBaseSpace Sequence Hub users manually review analyses and change the status of acceptable analyses as Ready For Delivery.
  9. Delivery of Data—Data is delivered using your preferred delivery mechanism, and the status is updated manually.