Preinstalled plugins

The following table lists and describes the plugins that are preinstalled with Torrent Suite™ Software.

Plugin name	Description
ampliSeqRNA plugin	Generates statistics, downloadable data files, and interactive visualizations that represent targeted RNA transcripts for sequencing runs that use the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit or Ion AmpliSeq™ RNA panels.
AssemblerSPAdes plugin	Performs an initial level analysis on assembly and provides metrics. The plugin is ideal for genomes less than 50 megabases in size.
coverageAnalysis plugin	Generates statistics and graphs to describe the level of sequence coverage that is produced for targeted genomic regions.
DataExport plugin	Exports data from a sequencing run to an external hard drive or a removable media, such as a USB drive.
ERCC_Analysis plugin	Indicates whether a problem exists with library preparation or sequencing for runs that use the ERCC RNA Spike‑In Mix.
FieldSupport plugin	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 your local Field Service Engineer or Technical Support.
FileExporter plugin	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 variantCaller plugin output files (when available), and compresses output files.
FilterDuplicates plugin	Removes duplicate reads and creates BAM files that do not contain the duplicate reads.
immuneResponseRNA plugin	Used to quantify gene expression levels for the Oncomine™ Immune Response Research Assay.
IonReporterUploader plugin	Transfers run results files to Ion Reporter™ Software. For details, see Integration with Ion Reporter Software.
molecular Coverage Analysis plugin	Generates statistics, downloadable data files, and interactive visualization of molecular coverage over targeted regions of the reference genome.
PGxAnalysis plugin	Use 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.
RunTransfer plugin	Transfers the signal processing output of a completed sequencing run from one Ion Torrent™ Server to another Ion Torrent™ Server, then runs an analysis of the transferred files on the receiving Ion Torrent™ Server.
sampleID plugin	Uses sample fingerprinting to identify any cross-contamination between samples or between barcodes in a run.
variantCaller plugin	Calls single-nucleotide polymorphisms (SNPs), multinucleotide polymorphisms (MNPs), insertions, deletions, and block substitutions in a sample across a reference or within a targeted subset of that reference.