Torrent Browser User Interface Guide

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Torrent Suite Software space on Ion Community

User Interface Guide TOC

Create a Template with Ion AmpliSeq.com Import

This page describes how to create a template based on an Ion AmpliSeq.com panel or on your Ion AmpliSeq.com custom design.

Integration with the variantCaller plugin

For community and fixed panels (not for custom panels) , the variantCaller plugin is pre-enabled i n your new template and the variantCaller plugin is pre-configured with parameters that are optimized for the panel. Later you can also add your own parameter customizations.

Types of Ion AmpliSeq templates

There are three types of Ion AmpliSeq templates, for DNA, RNA, and Exome. Human, animal and plant reference genomes are available. Start with the template group that matches your experiment type. Your choices of AmpliSeq.com panels to import are limited to panels that are related to that group type ( DNA, RNA, or Exome) .

Steps

Follow these steps to create a new template based on an Ion AmpliSeq.com panel:

1. Go to Plan > Templates .

2. Click the AmpliSeq.com button and select the type of panel you want to import: AmpliSeq DNA, AmpliSeq Exome, or AmpliSeq RNA.
3. If prompted to enter your ampliseq.com user name and password, do so.
4. Select your instrument and chip.
   
   
   
   

5. The Torrent Browser lists the available panels. Some panels do not have optimized Torrent Variant Caller parameter sets available for multiple chips and sequencers. A caution warning denotes choices for which optimized Torrent Variant Caller parameters have not be developed for the selected chip type, which may lead to suboptimal variant calls.

   A Show solutions which were not ordered link appears if you have unordered custom designs. Click this link if you want to import one of those designs.

   Enable the checkbox for the panel or panels you want to import, and click Import Selected .

   

6. The Torrent Browser opens a download and progress page:

   

   Refresh your browser to track the progress and see the completion status.

7. When the Status column shows "Completed", go back to the Templates tab, and you see the new template:

Optimized parameter settings

Use the import process described on this page in order to include optimized parameter settings in your new template.

Previous template creation process

The previous process to create a template from the Ion AmpliSeq Designer is described in Create a Template from AmpliSeq Designer . That older process is still supported but the Ion AmpliSeq.com Import process described here is recommended instead.

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