Torrent Suite™ Software includes many planned run templates to simplify your sequencing. Most templates have a corresponding Ion AmpliSeq™ panel. The following describe a template:

• A canned set of instructions for both your sequencing run and your post-sequencing data analysis.

• A digital protocol with specifications for almost your entire experiment, from sample preparation through sequencing, data analysis, and data export to other systems for additional analysis. (A plan template is missing only the sample name, from your experiment information.)

• A sample planned run that you can copy to quickly create actual planned runs with known defaults and settings.

• A reusable set of laboratory, sequencing, data analysis, and data management instructions.

These steps describe how a plan template fits into your Ion S5™, Ion S5™ XL, Ion PGM™ or Ion Proton™ sequencing workflow:

• Decide what sequencing application and sequencing product (such as an Ion AmpliSeq™ panel) you will use.

• Select a pre-installed template with defaults for your application and sequencing product, or create your own template from scratch. Then, customize your template.

• Copy the template to a new planned run, adding the name of the tissue sample to be sequenced. The Torrent Browser assigns your new plan a run code.

• Enter the run code directly on the Ion sequencing instrument to initiate the sequencing. The planned run automates the process from sequencing through data analysis and data handling.

With the planned run wizard, you can create a new planned run with only a few clicks and the entry of the sample name. With the Plan Multiple feature, you download a CSV and customize it to create multiple planned runs without using the planned run wizard.

Plan templates play an important role in enabling rapid throughput across your sequencing instrument. Templates also help reduce the chance of error, by listing the reagent kits used on the instrument.

The Plan > Templates screen contains your experiment templates. These include pre-installed product templates (for instance for products such as the Ion AmpliSeq™ panels) and as well as templates that you create, and areas for recently-used templates and ones you mark as favorites. Product templates contain the appropriate defaults for a product, including the default kits, BED files, and reference.