Torrent Suite Software 5.4 Help

Introduction

The Torrent Suite™ Software is organized according to the three main phases of the sequencing lifecycle:

  • Plan — The Plan tab contains both templates (reusable experiment designs) and planned runs (executable instructions for individual sequencing runs). Select the experimental design for a template that can be reused many times for sequencing runs. Template details include application, reference, BED files, project, plugins, and the export destinations for results files.

  • Monitor — View the status of your system and running jobs, including thumbnail quality graphs for current runs. The quality graphs provide near real-time information on your runs, so that you know early on about any instrument problems.

  • Data — View summaries of completed runs, detailed run reports, and plugin results. Also download output files, download the run report, review the planned run settings, and group result sets into projects for data management such as archiving or pruning of result files.

Templates are organized by research application (and by product for some applications):

Table 1.

Research application

Description

All

AmpliSeqDNA

For Ion AmpliSeq™ applications (DNA and exome), including the Ion AmpliSeq™ Any Genome, and Custom Ion AmpliSeq™ panels.

AmpliSeqRNA

For Ion AmpliSeq™ applications (RNA), including Oncomine Immune Response Research Assay.

DNA and Fusions

For Ion AmpliSeq™ applications such as Oncomine Focus Fusions, Oncomine Focus DNA & Fusions, Colon and Lung Research Panel v2.

Generic Sequencing

For your own applications that do not fit in the other categories. Use this research application to provide all the choices for the experiment. Your choices are not restricted based on a common application workflow.

Human Identification

For templates to run Applied Biosystems™ Precision ID set of panels.

Inherited Disease

For Ion Ampliseq Inherited Disease Panel and Oncomine BRCA Research Panels.

Oncology – ImmunoOncology

For all ImmunoOncology Applications. For example, Oncomine Immune Response Research Assay .

Oncology – Liquid Biopsy

For your liquid biopsy oncology research panels.

Oncology – Solid Tumor

For your solid tumor oncology research panels.

Pharmacogenomics

For Ion AmpliSeq™ Pharmacogenomics Research Panels imported from Ampliseq.com.

Reproductive

Ion Reproseq Aneuploidy applications.

RNA Seq

For RNA sequencing applications.

TargetSeq

For TargetSeq™ applications, with parameters optimized for hybridization-based target enrichment.

Whole-Genome

For whole genome sequencing applications, such as Ion ReproSeq™ Aneuploidy, which do not assume enrichment and do not require a target regions file.

16S rRNA Sequencing

For the Ion 16S™ Metagenomics kit.

16S Target Sequencing

For the Ion 16S™ Metagenomics kit.