• Introduction to Torrent Suite Software
  • Torrent Suite Software product information
  • Operating system compatibility
  • Browser compatibility
  • Hardware compatibility
  • Network and password security requirements
    • Network configuration and security
    • Password security
• Get started with Torrent Suite Software
  • Dashboard at a glance
  • News screen
  • User (Staff) versus Administrator (Superuser) roles
  • Plan a run
  • Register for a new user account
• Samples and Sample Sets
  • About samples and Sample Sets
  • Create a Sample Set manually
  • Create a Sample Set by importing samples from a CSV file
  • Create a samples file from a template
  • Sample information
    • View Sample Set attributes
    • Add a sample attribute to a sample
    • Manage sample attributes
    • Sample attributes
    • Sample Set definitions
  • View Ion AmpliSeq library preparation on an Ion Chef System run
  • Find a Sample Set
  • Sort Sample Sets
  • Edit a Sample Set
  • Delete a Sample Set
  • Create an Ion AmpliSeq on Ion Chef Sample Set
• Plan and execute an instrument run
  • Planned Runs
  • Planned Run templates
    • Planned Run templates for specific research applications
    • Create a custom Planned Run template
    • Create a Planned Run from a Planned Run template
    • Create a Planned Run without a Planned Run template
    • Search for a Planned Run template
    • Export a Planned Run template
    • Import a Planned Run template
    • Save a Planned Run template to Favorites
  • Steps in the workflow bar
    • Ion Reporter step in the workflow bar
    • Research application step in the workflow bar
    • Kits step in the workflow bar
      • Advanced Settings—Kits step in workflow bar
      • About the Mark as Duplicates Reads option
    • Plugins step in the workflow bar
    • Projects step in the workflow bar
    • Plan step in the workflow bar
  • Review Planned Run settings
  • Import panel files and parameters
    • Link your Ion Torrent Server account to AmpliSeq.com
    • Import Planned Run template parameters
    • Manually upload panel files
    • Copy an analysis parameter set
  • Create Planned Runs
    • Plan by Sample Set
    • Create a Planned Run with Sample Sets
      • Command Line Args (Advanced) screen
    • Create a Planned Run for mixed samples with a Planned Run template
  • Create multiple Planned Runs
    • Create multiple Planned Runs for non‑barcoded libraries
    • Create multiple Planned Runs for barcoded libraries
  • Planned Runs list
    • Manage Planned Runs
    • Planned Run status
      • Manually change Ion Chef Instrument run status
    • Execute a Planned Run on a sequencer
    • Transfer a Planned Run to another Ion Torrent Server
• Monitor runs in progress
  • Monitor a sequencing run
  • Monitor an Ion Chef run
  • View data for runs in progress
  • Auto Refresh the Monitor tab
  • Review the Planned Run settings
  • Stop an analysis job
  • View system memory usage
• Review and manage run reports
  • About run reports
  • Search for a run report
  • Open a run report
    • Review unaligned reads
      • Run report metrics before alignment
    • Review aligned reads
      • Quality following alignment
        • Aligned read length calculation
        • Alignment
        • Reads used for alignment
        • Predicted quality (Q20)
          • Per-base quality score system
          • Quality score predictors
      • Run report metrics after alignment
    • Run report metrics
      • Throughput considerations
      • ISP loading density
      • Total reads
        • Well classification
        • Read filtering and trimming
      • Read length
      • Key signal
    • Output files
      • Download output files
      • View and download barcode reports
    • Download a run report summary PDF
  • View details about completed runs
    • View test fragments for a completed run
    • View consumables used in a completed run
    • View the summary for an Ion Chef Instrument run
    • View the calibration report for a completed run
    • View analysis details for a completed run
    • View software versions used in a run
  • Organize run results with projects
    • Search for projects by name
    • Add a project to a Planned Run
      • Add selected results to another project
    • View result sets in a project
    • Compare reports of runs in a project
    • Manage data for result sets in projects
    • Combine aligned reads from multiple run reports
    • Download a CSV file of metrics
      • Analysis metrics file fields
    • Remove a result set from a project
  • Reanalyze a run
    • Change the default alignment reference
  • Edit a run report
    • Add or change barcoding for a completed run report
  • Set the Completed Runs & Reports screen to automatically refresh
• Manage plugins for data analysis
  • Plugin configuration
    • Configure plugins globally
    • Configure a plugin to run automatically
  • Run a plugin manually from the sequencing run report
  • Download a plugin report PDF
  • View plugin run status
    • Stop a plugin run
    • Open a plugin log
    • Delete plugin results from a run report
    • Rescan a plugin
  • Preinstalled plugins
    • ampliSeqRNA plugin
      • ampliSeqRNA plugin configuration
      • Review ampliSeqRNA plugin results
        • ampliSeqRNA plugin reports
    • AssemblerSPAdes plugin
      • AssemblerSPAdes plugin configuration
      • Review AssemblerSPAdes plugin results
      • Analysis metrics file fields
    • coverageAnalysis plugin
      • coverageAnalysis plugin configuration
      • Review coverageAnalysis plugin results
        • Reads statistics 
        • Example charts generated by the coverageAnalysis plugin
        • Output files generated by the coverageAnalysis plugin
    • DataExport plugin
      • DataExport plugin configuration
      • Review DataExport plugin results
    • ERCC_Analysis plugin
      • ERCC_Analysis plugin configuration
      • Review the ERCC_Analysis plugin results
        • Interpret the ERCC Dose Response plot 
        • View ERCC transcript details
        • Definitions
      • ERCC resources
    • FieldSupport plugin
    • FileExporter plugin
      • Configure the FileExporter plugin
      • Review FileExporter plugin results
    • FilterDuplicates plugin
      • Review FilterDuplicates plugin results
    • immuneResponseRNA plugin
      • immuneResponseRNA plugin configuration
      • Review immuneResponseRNA plugin results
        • Downloadable reports
    • IonReporterUploader plugin
    • molecular Coverage Analysis plugin
      • molecular Coverage Analysis plugin configuration
      • Review molecular Coverage Analysis plugin results
        • Molecule statistics
        • Example charts generated by the molecular Coverage Analysis plugin
        • Output files generated by the molecular Coverage Analysis plugin
    • PGxAnalysis plugin
      • Review PGxAnalysis plugin results
    • RunTransfer plugin
      • RunTransfer plugin configuration
      • Review RunTransfer plugin results
    • sampleID plugin
      • Review sampleID plugin results
    • variantCaller plugin
  • Plugins available on Connect
    • RNASeqAnalysis plugin
      • RNASeqAnalysis plugin configuration
      • Review RNASeqAnalysis plugin run results
        • Downloadable reports for individual RNASeqAnalysis plugin barcodes
        • Individual barcode view
        • Distribution plots
        • Correlation heatmap
        • Correlation plot
        • Gene heatmap
        • Isoform heatmap
    • smallRNA plugin
      • smallRNA plugin
      • Review smallRNA plugin results
• Variant calls in Torrent Suite Software
  • About the variantCaller plugin
  • Run the variantCaller plugin
    • Configure the variantCaller plugin to run by default after every run
    • Configure the variantCaller plugin to run as part of a Planned Run
    • Run the variantCaller plugin manually
    • variantCaller plugin configuration
  • Create a custom configuration for the variantCaller plugin
  • Apply configuration settings to specific barcodes
  • Create and use a custom parameters setting
  • Review variantCaller plugin run results
    • Detailed variantCaller plugin report
    • Variant Calls by Allele table
    • View allele annotations 
    • View coverage metrics 
    • View quality metrics
    • Export variant calls to a file
    • Troubleshoot variantCaller plugin results
      • Find false negatives with an alignment viewer
      • Find false negatives by using the variantCaller plugin report
      • Fix false positives
      • Export files for troubleshooting
  • Save adjusted parameters to a variantCaller plugin configuration
  • variantCaller plugin advanced parameters
    • Torrent Variant Caller module advanced settings
    • FreeBayes module advanced settings
    • Long INDEL Assembler module advanced settings
    • Advanced argument settings
• Integration with Ion Reporter Software
  • About Ion Reporter Software
  • Install the IonReporterUploader plugin on a Ion Torrent Server
  • Set up an account for IonReporterUploader plugin
  • Automatically transfer Torrent Suite Software output to Ion Reporter Software
    • Manage the Ion Reporter Software analysis workflow list
    • Sample gender
  • Run the IonReporterUploader plugin manually
  • IonReporterUploader plugin configuration
  • IonReporterUploader plugin file transfer progress
    • View IonReporterUploader plugin status details
    • Delete IonReporterUploader plugin report files
  • Tune IonReporterUploader plugin speed parameters
  • Review IonReporterUploader plugin results
    • Torrent Suite Software output and Ion Reporter Software analysis phases
  • IonReporterUploader command-line utility
    • Download IonReporterUploader command-line utility
    • Run IonReporterUploader command-line utility
• References management
  • About references
  • Reference sequences
    • hg19 reference
      • Hard masked PAR regions in chromosome Y
      • Three positions with ambiguity codes
      • Chromosome M reference sequence
    • GRCh38 reference
    • Import reference sequence files
      • Guidelines for importing custom reference sequence files
      • Import a preloaded reference sequence file
      • Import a custom reference sequence file
    • View a reference sequence file
    • Edit reference sequence file properties
    • Permanently delete a reference sequence file
    • Obsolete reference sequences
  • Target regions and hotspots files
    • Guidelines for using target regions and hotspots files
    • View and manage target regions files
    • View and manage hotspots files
    • Modify a BED file
    • Upload a target regions file
    • Upload a hotspots file
    • BED file formats and examples
      • Target regions BED file formats
        • 3-column target regions BED file format
        • 4-column target regions BED file format
        • 6-column target regions BED file format
        • 8-column target regions BED file format
        • BED files generated by Ion AmpliSeq Designer custom designs
      • Hotspots file format
        • HotSpotAlleles field
        • Partial example of a hotspots BED file
        • Extended BED Detail format
        • Examples from BED files in the Extended BED Detail format
        • Merged Extended BED Detail format files
          • Example 1
          • Example 2
        • Score and strand fields in uploaded hotspot BED files
      • RNA fusions BED file formats and examples
        • Track line
        • Example BED file entries
  • Test fragments
    • View test fragment details
    • Add a custom test fragment
    • Edit or delete a custom test fragment
  • Barcodes and barcode sets
    • View a DNA barcode sequence
    • Download a DNA barcode set CSV file
    • Add a custom DNA barcode set
      • DNA barcode set CSV file setup
    • Delete a custom DNA barcode set
  • Upload history
• Data management
  • View disk usage parameters
  • View category statistics
  • View active data management jobs
    • Error messages
    • Disk full message
  • Search for run reports with disk usage status
  • Keep run report data
  • Import data for data transfers or restoration
  • View the data management actions log
• Supported software modules
  • Analysis pipeline overview
  • BaseCaller module and barcode classification overview
    • Overview of the BaseCaller module functionality
      • Notes about barcode classification and barcode filtering
    • Ion Torrent BAM format
    • Custom BAM recorder tags
    • BaseCaller module arguments
      • About BaseCaller module parameters
      • Barcode classification parameters
        • Cutoff setting
        • Separation setting
      • Other public parameters
    • About barcodes
    • Troubleshooting barcode classification issues
      • Explanation of fields in the BaseCaller JSON file
        • Barcode bias
        • Barcode distance histogram
        • Barcode errors histogram
        • Barcode match filtered
        • Filtered
        • Read count
  • TMAP modules
    • Mapping modules
    • Find the TMAP command for a specific analysis
    • TMAP examples
    • Global options used by all TMAP modules
    • Global pairing options
    • TMAP map1 options
    • TMAP map2 options
    • TMAP map3 options
    • TMAP map4 options
    • TMAP mapvsw options
    • TMAP alignment refinement
• Administer Torrent Suite Software
  • Open the Site Administration screen
  • Install Torrent Suite Software
    • Manage Torrent Suite Software user accounts
      • Approve or reject a new user account
      • Modify a user account
      • Delete a single user account
      • Delete multiple user accounts
      • Create a new administrator account to change a password
    • Add customer support contacts
    • Change the time zone for the Ion Torrent Server
    • Change the displayed server name
    • Lock current Torrent Suite Software version
  • Update Torrent Suite Software
    • Update Torrent Suite Software
    • Check for off-cycle updates
    • Enable off-cycle product updates
    • Install off-cycle bundles without Internet access
  • Install or upgrade plugins
    • Enable an installed plugin
    • Configure plugins globally
    • Update off-cycle release plugins
    • Uninstall a plugin
  • Manage disk usage
    • View disk usage parameters
    • Ion instrument data types
    • Archive or delete data automatically
    • Manually export run data
    • Manually archive run data
    • Manually delete selected data from a run report
    • Increase file storage and available disk space
      • Connect to a Torrent Storage NAS (Network Attached Server) device
        • Connect directly to a Torrent Storage NAS (Network Attached Server) device
        • Connect over a network to a Torrent Storage NAS (Network Attached Server) device
        • Monitor the Torrent Storage NAS (Network Attached Server) device
      • USB drives
        • Mount a USB drive
        • Unmount a USB drive
    • Dataflow file sizes
      • Dataflow using the 200-bp kit on the Ion GeneStudio S5 Plus System, Ion GeneStudio S5 Prime System, and Ion S5 XL System
      • Dataflow using the 400-bp kit on the Ion GeneStudio S5 Plus System, Ion GeneStudio S5 Prime System, and Ion S5 XL System
      • Dataflow using the 400-bp kit on the Ion PGM Sequencer
      • Dataflow using the 200-bp kit on the Ion PGM Sequencer and Ion Proton Sequencer
  • Set up flexible workflows
    • View sequencing runs on multiple sequencers with Ion Mesh
    • Transfer a Planned Run to a Ion Torrent Server with Ion Mesh
    • Track Ion Chef Instrument flexible workflows for Ion 550 chips with Ion Mesh
  • Data backup and restore locations
    • Restore the PostgreSQL Database
  • Manage telemetry services
    • Axeda Remote System Monitoring (RSM)
      • Remote access for troubleshooting
      • Axeda RSM agent overview
      • Port assignments
    • Deep Laser
    • Data automatically collected by the telemetry services
      • Ion Torrent Server data
      • Ion PGM data
      • Ion S5, Ion Proton, and Ion GeneStudio S5 System data
  • Administration with command-line utilities
    • Monitor disk space
    • Change the hostname
    • Change the time zone
    • Add an HTTP proxy
    • Alternate checks
• Screen descriptions
  • User and account settings screen
  • Analysis Parameters screen
  • Configure screen
  • Ion Reporter configuration screen
  • Plugins screen
  • Updates screen
  • References Sequences screen
  • Services screen
  • Planned Runs screen
  • Samples screen
  • Templates screen
  • Runs in Progress screen
  • Ion Chef screen
  • Completed Runs & Reports screen
  • Run Report screen
  • Projects screen
  • Data Management screen
• Troubleshooting
  • Troubleshooting resources
  • Troubleshoot Torrent Suite Software
    • Get technical support files for a completed run
    • Troubleshoot a sequencing run
    • Customer Support Archive (CSA)
      • Generate a customer support archive
      • Customer support archive contents
    • Troubleshoot IonReporterUploader plugin account setup
    • Troubleshooting file import/upload errors
  • Troubleshoot Ion Torrent Server
    • Check crawler and job server status
      • Queue status
    • Verify network connectivity and name resolution
    • Verify the Ion Torrent Server IP address
    • Troubleshoot and configure the time service
    • Verify file transfer
    • View system support diagnostics
    • View instrument diagnostics
    • Restart services
    • Further investigation and problem resolution
• Documentation and support
  • Customer and technical support
  • Limited product warranty
• Legal