Thermo Fisher Scientific Ion Reporter User Manual
RELEASE NOTES
Ion Reporter™ Software 5.16 Release Notes
Pub. No. MAN0019149 Rev. C.0
Contents
Revision History .............................................................................................................................. 2
New Features in Ion Reporter™ Software 5.16 .............................................................................. 3
Analysis workflow variant calling and annotation improvements and feature enhancements for
assays and panels ..................................................................................................................................... 3
Improved RAID status capabilities on Ion Reporter™ Server ................................................................... 3
Launch multiple Immune Repertoire workflows simultaneously for each sample ................................. 3
Change to MAF filter in Ion Reporter™ Software .................................................................................... 4
New adjustable parameters to customize Immune Repertoire analysis workflows ............................... 4
Launch multiple Immune Repertoire workflows simultaneously for each sample ................................. 4
NCBI 16S sequence database included in Ion AmpliSeq™ Microbiome Health workflows ..................... 4
Fusion calling parameter to allow potential increase in sensitivity ......................................................... 4
AmpliSeq™ Colon and Lung analysis workflow configuration settings have been updated ................... 4
Ion AmpliSeq™ Microbiome Health Research Panel ............................................................................... 4
BRCA analyses enhancements ................................................................................................................. 5
New data column for analysis results from AmpliSeq analysis workflows .............................................. 5
User experience improvement ................................................................................................................ 5
Data and annotation source updates ...................................................................................................... 5
End of life for Ion Reporter™ Software 5.4 analysis workflows ............................................................... 5
Java version required for the Integrative Genomics Viewer (IGV) .......................................................... 5
Ion AmpliSeq™ Designer access code is required to import panel designs ............................................. 6
Software assessment service ................................................................................................................... 6
Issues fixed in Ion Reporter™ Software 5.16 ................................................................................. 7
Known issues and limitations in Ion Reporter™ Software 5.16 ..................................................... 9
Documentation ............................................................................................................................. 15
Compatibility with Torrent Suite™ Software ............................................................................... 16
IonReporterUploader plugin ........................................................................................................ 17
Ion Reporter™ Software command-line utility (IRUCLI) .............................................................. 18
IonReporterUploader plugin configuration.................................................................................. 18
Ion Reporter™ Server: Update Operating System ....................................................................... 18
Update Ion Reporter™ Server Software to 5.16 .......................................................................... 19
For Research Use Only. Not for use in diagnostic procedures.
Revision History
Revision
Date
Description
C.0
12 March 2021
Additional information added to: Ion Reporter™
Change in MAF filtering
B.0
17 December
Updated release notes for Ion Reporter™ Server
improvements
A.0
29 October
New release notes for Ion Reporter™ Software 5.16.
Server 5.16 new features:
• Ion AmpliSeq™ CarrierSeq ECS Panel
• Oncomine™ Comprehensive Assay Plus
2020
2020
5.16:
• Fixed issues
o IR-46893
o IR-46975
o IR-46988
o IR-46979
o IR-47057
• New feature:
o Ion Reporter™ Server
administrators now have more
messaging and information on
RAID status.
• Feature removed – Myeloid Assay
Ion Reporter ™ Software 5.16 Release Notes 2
New Features in Ion Reporter™ Software 5.16
Analysis workflow variant calling and annotation improvements and feature enhancements
for assays and panels
• Ion AmpliSeq™ Microbiome Health Research Panel: detects microbial species via 16S and target
species-specific amplicons with single and multi-analysis comparisons, using a variety of
common databases and QIIME2 functionality
• Oncomine™ tumor specific panels: analysis of focused, pre-designed or customized cancer
panels relevant for clinical cancer research
• Oncomine™ Comprehensive Assay Plus:
Comprehensive genomic profiling with analysis of low-frequency somatic variants (SNPs, Indels,
CNVs) from over 500 genes, tumor mutation burden (TMB), Loss-Of-Heterozygosity, and
microsatellite instability (MSI), and includes the following new features:
• Exon-level Loss detection
• %LOH and gene-level LOH detection
• Automatically calculated tumor cellularity
• Separate analysis workflows for samples prepared manually or on the Ion Chef instrument
• Improvements in MSI detection
• FusionSync technology covering >1300 isoforms with 49 fusion drivers, enabling: fusion
detection from low input samples, detection of low level of fusion transcripts, and the ability
to detect novel fusions for driver genes.
• Ion AmpliSeq™ CarrierSeq ECS Panel provides detection and analysis of single nucleotide
variants (SNVs), insertion/deletions (INDELs), and copy number variants (CNVs) associated with
418 inherited disorders from a single assay. CarrierSeq ECS - 530 - w1.3 - Single Sample and
CarrierSeq ECS - 540 - w1.3 - Single Sample workflows, released with Ion Reporter v5.16,
contains the following improvements:
• SNV/INDEL genotyping
• Unified hotspot list of >36,000 SNVs and INDELs (combined a CarrierSeq hotspot list of
>28,000 with a Igentify Curated hotspot list)
• Parameter optimization, SVB Improvements, excluded high frequency NO CALL Hotspots,
updated Hotspot Annotation
• CNV calling
• Confidence filtering (threshold of 6.9)
• HMM sensitivity and specificity improvements
• Improved baseline for gene conversion algorithm calling disorders from a single assay
Improved RAID status capabilities on Ion Reporter™ Server
Ion Reporter™ Server administrators now have more messaging and information on RAID status. To view
the RAID status, in the Admin tab, click System Services, then click RAID Status.
Launch multiple Immune Repertoire workflows simultaneously for each sample
When you plan runs in Torrent Suite™ Software you can choose to select multiple immune repertoire
analysis workflows to launch with each uploaded sample.
Ion Reporter ™ Software 5.16 Release Notes 3
Change to MAF filter in Ion Reporter™ Software
In Ion Reporter™ Software 5.14 and earlier, the MAF filter searches MAFs of all alleles that are
associated with a locus. Alleles at the locus found by the filter are returned as filtered results if they fall
within the specified MAF range (except rma=1). In Ion Reporter™ Software 5.16, the MAF filter searches
only the allele(s) that are specified by the genotype (excluding rma=1). The allele-based MAF filter
results can be downloaded as Filtered Variants.
However, the Analysis Results screen in Ion Reporter™ Software 5.16 continues to show the locus-based
MAF values when no MAF filter is applied . As a result, users may observe some variants which have
displayed MAF values within the filtered in range are not returned by the new MAF filter on Analysis
Result screen. To avoid the discrepancy, use allele view, which is not expected to have this issue because
there is only one variant allele shown on each line.
New adjustable parameters to customize Immune Repertoire analysis workflows
You can customize immune repertoire analysis workflows with adjustable parameters.
Launch multiple Immune Repertoire workflows simultaneously for each sample
When you plan runs in Torrent Suite™ Software you can choose to select multiple immune repertoire
analysis workflows to launch with each uploaded sample.
NCBI 16S sequence database included in Ion AmpliSeq™ Microbiome Health workflows
Ion AmpliSeq™ Microbiome Health Research Assay workflows now include the option to select the NCBI
16S sequence database for analysis.
Fusion calling parameter to allow potential increase in sensitivity
Fusion calling in analysis workflows for AmpliSeq HD and TagSeq panels and assays can now be done in
one of two ways with a new optional fusion calling parameter. You now have the option to select how
Present calls are made by: 1) using threshold settings for either molecular (family) counts or read
counts, or 2) selecting a setting that requires the thresholds that you configure to be reached for both
molecular and read counts. The default setting of this new parameter depends on the panel and analysis
workflow but can now be edited to choose one or the other method. The types of counts used to call
each fusion as Present are indicated in the analysis results. The impact of this parameter, when turned
on to use either molecular counts or read counts, is the potential for increased fusion call sensitivity.
AmpliSeq™ Colon and Lung analysis workflow configuration settings have been updated
AmpliSeq™ Colon and Lung analysis workflow configuration settings have been updated to improve
performance.
Ion AmpliSeq™ Microbiome Health Research Panel
• Data sorting is improved in the 16S rRNA Gene source data table in analysis results that use the
Ion AmpliSeq™ Microbiome Health Research Panel and analysis workflows. By default, data is
sorted with Family-level abundance results, descending, at the top, with the secondary sort by
Genus-level abundance, descending, within Families. You can optionally choose to sort by
Family name, with the secondary sort by Genus-level abundance, descending, within the
alphabetically sorted Families.
• The species abundance bar graphs and heat maps now include a Phylum level data, in addition
to Family and Genus.
Ion Reporter ™ Software 5.16 Release Notes 4
BRCA analyses enhancements
• Oncomine BRCA troubleshooting: Gene_Deletions.xls file is now downloadable.
• Summary table included in BRCA visualizations provides access to more data
New data column for analysis results from AmpliSeq analysis workflows
• A Raw Coverage data column is now included in analysis results for AmpliSeq analysis
workflows.
User experience improvement
• The “IRGV” tab has been renamed to “IRGV and Generate Report” tab. Users can visualize data
in the IRGV data and generate a report that contains the data from the same tab.
Data and annotation source updates
• Updated controlled vocabulary for cancer types
• Updated hg19 and GRCh38 annotation sources
End of life for Ion Reporter™ Software 5.4 analysis workflows
Ion Reporter™ Software 5.4 analysis workflows are now retired from the Ion Reporter™ Software 5.16.
Version 5.4 analysis workflows will also be unavailable after servers are upgraded Ion Reporter™
Software 5.16. Analyses that are launched through analysis workflows from Ion Reporter™ Software 5.4
and earlier will continue to be available to open and create reports for in the latest version of Ion
Reporter™ Software. Each new version of Ion Reporter™ Software will continue to retire at least one of
the earliest versions of the currently released Ion Reporter™ Software analysis workflows.
Java version required for the Integrative Genomics Viewer (IGV)
Java 8 is required to launch IGV from Ion Reporter Software. Java 8 is included with the software. If you
are running Java 9 or later, you must have Java 8 also for JNLP to work correctly.
Ion Reporter ™ Software 5.16 Release Notes 5
Ion AmpliSeq™ Designer access code is required to import panel designs
An AmpliSeq Designer access code has been added to enhance security for the import of panel designs
from ampliseq.com. You must authenticate your account by providing ampliseq.com username and the
access code to import panel designs for Ion AmpliSeq™ and Ion AmpliSeq™ HD Made-to-Order, OnDemand, or Ready-to-Use research panels from ampliseq.com into Ion Reporter™ Software. The
imported files are used when you create an analysis workflow for use with the Ion AmpliSeq™ Designer
panels.
You are required to generate an access code for your ampliseq.com account just one time, if you save
the access code when it is generated. If you do not save the access code, you have the option to
regenerate a new one when you sign in again on ampliseq.com. You will be required to set a new access
code when the code expires.
1. Go to ampliseq.com and sign into your account.
2. Click My Account > Manage Access Code.
3. Generate an access code.
a. In the Manage Access Code dialog box, select an Access Code Expiration in the dropdown
menu.
b. Click Generate.
c. Click Copy to Clipboard.
The access code is available for use on the clipboard.
d. (Optional) Click Save to save the access code for use when you return to ampliseq.com.
You can now use the access code to import panel files or planned runs from ampliseq.com.
For more information, see the Ion Reporter™ Software help system.
Software assessment service
Assessment to help optimize Ion Reporter(TM) workflows for new and established assays on a new
version of Ion Reporter™ Software. Contact your bioinformatics support team to learn more.
Ion Reporter ™ Software 5.16 Release Notes 6
Loading...