Torrent Browser User Interface Guide

Torrent Suite Software space on Ion Community

The Template and Planned Run Wizard

When you create a new template or a new planned run, a wizard guides you through the process. You can begin by copying one of the pre-installed product templates, and then the wizard is populated with defaults that are compatible with that product.

The same wizard supports both new templates and new planned runs.

The template wizard guides you through several pages where you can approve or change each pre-populated default.

The wizard pages and chevron names correspond to the areas of information seen when you review a template or plan (see Example template and planned run information ).

You can navigate to a wizard page by clicking on its chevron, in addition to clicking the Next button.

Example template and planned run information

The following shows the type of information contained in both a template and a planned run. This format is used by the wizard Review Run Plan and Review Template buttons and the Plan > Planned Run page review option. Sequencing sample names and run names are not shown in these reviews, but are present in planned runs. Sample names and run names are not contained in template information.

Differences between templates and planned runs

Templates and planned runs have much the same information.

Templates come first. Planned runs are created from templates.
Templates do not have sample names and run names. Planned runs do contain these names.
Planned runs are executable on the sequencing instrument, because they contain sample names and run names.
A template is a sample planned run. From a template, you can create many planned runs. Each resulting planned run is already customized for your research and can quickly be created from your template you add only the sample name and the run name.
The planned run wizard opens in the last page, so that if you accept all the template settings, all you need do is supply are the run name and sample names and save the new planned run.
The last page of the wizard is different for templates and planned runs. The planned run last page requires the run name and sample names. (Templates do not contain this information.)

The wizard pages for a template and a planned run are the same except for the last page. The planned run last page requires the run name and sample names.

Template wizard:

Planned run wizard:

Plan by sample:

Start the wizard

For both templates and planned runs, you start the wizard from the Plan > Templates page. The steps to start the wizard depend on whether you want to create a planned run from generic application template or an existing template, or create a template from generic application template or an existing template.

How you start the wizard is important, especially if your sequencing workflow uses common sequencing products. Pre-installed templates are available for these common sequencing products:

Ion AmpliSeqCancer Hotspot Panel v2.0
Ion AmpliSeqComprehensive Cancer Panel
Ion AmpliSeqCancer Panel Primer Pool Kit
Ion AmpliSeqInherited Disease Panel
Ion AmpliSeq Any Genome Panel

If you start with a pre-install product template, your new template or planned run has the correct settings for the product.

Templates

To create a new template from a generic application template, click the Add New Template link next to the application name. This template has the default for the application type, but is not customized for a specific panel.

To create a new template from an existing template, click the gear menu in that template's row and click Copy:

Planned runs

To create a new planned run from a generic application template, click the Plan New Run link next to the application name.

To create a new planned run from an existing template, click the gear menu in that template's row and click Plan Run .

Plan by sample set

The plan by sample set feature supports Ion Reporter Software users by automatically filling out the sample information in the run plan wizard. When opened from a multi-sample sample set, the wizard has an additional chevron named Barcoding. The Barcoding chevron contains the sample information and Ion Reporter Software workflow information.

The wizard for plan by sample set is started from the gear menu menu on the Plan > Samples tab, with the Plan Run option: