ampliSeqRNA

Generates statistics, downloadable data files and interactive visualizations that represent targeted RNA transcripts for sequencing runs that use the AmpliSeq™ Transcriptome Human Gene Expression Kit, AmpliSeq™ RNA panel, and custom RNA panels.

For details, see ampliSeqRNA plugin.

AssemblerSPAdes

Performs an initial level analysis on assembly and provides metrics. The plugin is ideal for genomes less than 50 megabases in size.

For details, see Assembler SPAdes plugin.

coverageAnalysis

Generates statistics and graphs to describe the level of sequence coverage that is produced for targeted genomic regions.

For details, see coverageAnalysis plugin.

DataExport

Exports data from a sequencing run to an external hard drive or a removable media, such as a USB drive.

For details, see Data Export plugin.

ERCC_Analysis

Reveals whether analyses that use ERCC RNA Spike-In Controls indicate a problem exists with either the library preparation or the sequencing instrument run.

For details, see ERCC Analysis plugin.

FieldSupport

Provides assistance with technical support. Enable and run this plugin only under the guidance of Thermo Fisher Scientific Technical Support. If you have questions about this plugin, contact technical support or your Field Application Scientist.

FileExporter

Customizes the output file names of an analysis run. This plugin allows you to rename output files. Also generates a FASTQ format file of the analysis output, renames Variant Caller plugin output files (when available), and compresses output files.

For details, see FileExporter plugin.

FilterDuplicates

Removes duplicate reads and creates BAM files that do not contain the duplicate reads.

For details, see FilterDuplicates plugin.

immuneResponseRNA plugin

Use the immuneResponseRNA plugin to quantify gene expression levels for the Oncomine™ Immune Response Research Assay.

For details, see immuneResponseRNA plugin.

Ion Reporter Uploader

Transfers run results files to your organization in Ion Reporter™ Software (available under a separate license).

For details, see Integration with Ion Reporter Software.

PGxAnalysis

Used with the Ion AmpliSeq™ Pharmacogenomics Research Panel, which is a targeted gene panel that allows the interrogation of Pharmacogenomics variants in samples for genotyping and CYP2D6 copy number detection.

For details, see PGxAnalysis plugin.

RNASeqAnalysis

Analyzes cDNA reads. This plugin is an RNA transcript alignment and analysis tool for use with the reference genomes hg19 and mm10.

For details, see RNASeqAnalysis plugin.

RunTransfer

Transfers the signal processing output of a completed sequencing run from one Torrent Server to another Torrent Server, then runs an analysis of the transferred files on the receiving Torrent Server.

For details, see RunTransfer plugin.

sampleID

Uses sample fingerprinting to identify any cross-contamination between samples or between barcodes in a run.

For details, see sampleID plugin.

variantCaller

For details, see variantCaller plugin.