# Choose Your Entry Point

You can launch the analysis from three different starting points depending on your situation. Use the table below to decide which path fits your workflow:

|                                   | Run Planner                                | BSSH Application                                                                             | ICA Pipeline                                                                                      |
| --------------------------------- | ------------------------------------------ | -------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------- |
| **Best for**                      | New sequencing runs with automated launch  | Existing data or tumor-normal pairs                                                          | Advanced workflows, multi-run merging, batch options                                              |
| **Hands-on effort**               | Minimal — push-button                      | Low                                                                                          | Low                                                                                               |
| **Analysis modes**                | Tumor-only                                 | Tumor-only and tumor-normal                                                                  | Tumor-only and tumor-normal                                                                       |
| **Input types**                   | BCL files from sequencer + Target BED file | FASTQ, BAM, CRAM files + Target BED file + Systematic noise file + (optional) Block-zone BED | FASTQ, BAM, CRAM, ORA files + Target BED file + Systematic noise file + (optional) Block-zone BED |
| **Connected Insights compatible** | Yes                                        | Yes                                                                                          | Yes                                                                                               |

{% hint style="success" %}
**Recommendation.** For the best end-to-end experience, use an ICA account. The ICA basic account gives you access to BaseSpace Sequence Hub (BSSH) and unlocks all three entry points.
{% endhint %}

## When to Use Each Entry Point

{% tabs %}
{% tab title="Run Planner" %}
**Use Run Planner when** you are planning a new sequencing run and want the analysis to launch automatically when sequencing completes.

* One-click setup from BSSH
* Tumor-only analysis only
* Auto-launches both the Baseline Builder (Stage 1) and the DRAGEN Somatic for IDT Custom panels (Stage 2)
  {% endtab %}

{% tab title="BSSH Application" %}
**Use the BSSH application when** you have existing FASTQ, BAM, or CRAM data, or when you need tumor-normal analysis.

* Supports tumor-only and tumor-normal modes
* Use existing data; no need to start from a new sequencing run
* More control over pipeline configuration than Run Planner
  {% endtab %}

{% tab title="ICA Pipeline" %}
**Use the ICA pipeline when** you need advanced control, multi-run merging, batch options, or ORA-format input.

* Supports all input types including ORA
* Batch available
* Required for multi-run merging workflows
  {% endtab %}
  {% endtabs %}


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