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

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.

When to Use Each Entry Point

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)

BSSH Application

ICA Pipeline