# Automatic Data Flow

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

![See explanation for each numbered data-flow step step below...](https://330234082-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2Fg3bE5PSqw4Kkyc9yUsgB%2Fuploads%2Fgit-blob-71fdf1b1789d9b9154ed0d129050683eecf6ac42%2Fauto-data-flow.png?alt=media)

1. Biosample Workflow File Import—Add biosamples, library prep instructions, and analysis workflow instructions via a biosample workflow file. BaseSpace Sequence Hub creates new biosamples and schedules analyses.
2. 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.
3. Library Prep—BaseSpace Sequence Hub reports library prep status and QC.
4. Automatic Lane QC—BaseSpace Sequence Hub automatically performs lane QC on the new sequencing data based on the configured lane QC thresholds. 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 Generation—BaseSpace 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 Launch—BaseSpace 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 biosamples that are QC failed or are associated with a different project. Data sets can originate from multiple flow cells or other uploads.
7. Automatic Analysis QC— BaseSpace Sequence Hub automatically performs analysis QC after analysis is complete.
8. Mark Analyses for Delivery—BaseSpace Sequence Hub users manually review analyses and change the status of acceptable analyses as Ready For Delivery.
9. Deliver Data—Deliver data using your preferred delivery mechanism, and mark the data as delivered.


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://help.basespace.illumina.com/automate/automatic-data-flow.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.