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Thermo Fisher Scientific Genexus Software 6.8 User guide

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For Research Use Only. Not for use in diagnostic procedures.
Genexus™ Software 6.8
USER GUIDE
Publication NumberMAN0026409
Revision D.0
Life Technologies Corporation | 200 Oyster Point Blvd | South San Francisco, California 94080 USA
For descriptions of symbols on product labels or product documents, go to thermofisher.com/symbols-definition.
Revision history:Pub.No.MAN0026409
Revision Date Description
D.0 11 May 2023
• Added information about a message that occurs in the software when a Nucleic Acid to Result run
is planned.
• Corrected a typo for the name of GAF filter.
• Minor edits for clarification
C.0 6 March 2023
Updates to the user guide are as follows:
• Added recommendation for use of password-protected SSH private keys.
• Replaced references to "Genexus™ Software server" with "Genexus Integrated Sequencer".
• Added information about Chromosome arm-level alterations to the table in the topic "Summary of
variant types and examples of standardized variant names."
• Removed information for parameter that is not supported for getReportTemplates web API call.
• Made minor edits to grammer, punctuation and spelling.
• Updated "View key findings" topic to remove mention of coverage graphs, which are not supported
inGenexus™ Software 6.8.
• Updated "Key findings" topic to remove mention of coverage plots, which are no longer supported
in Genexus™ Software 6.8.
• Updated definition of ABSENT in "SNVs/Indels table" topic for clarity.
• Added to description of what is seen in details section for step 3 in "View hotspot file details" topic.
• Correction to typo for name of GAF filter
B.0 27 July 2022
The two following updates were made to Genexus™ Software 6.8 User Guide. Correction of information
about default setting in the topic named "Set a schedule to permanently delete files." Change of website
name to "Connect" instead of "Thermo Fisher Connect".
A.0 11 July 2022 New Genexus™ Software 6.8 User Guide.
The information in this guide is subject to change without notice.
DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC. AND/OR ITS AFFILIATE(S) WILL NOT BE
LIABLE FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR
ARISING FROM THIS DOCUMENT, INCLUDING YOUR USE OF IT.
Important Licensing Information: This product may be covered by one or more Limited Use Label Licenses. By use of this product,
you accept the terms and conditions of all applicable Limited Use Label Licenses.
TRADEMARKS: All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified.
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Amazon Web Services is a trademark of Amazon.com, Inc. or its aliates in the United States and/or other countries.
©2023 Thermo Fisher Scientific Inc. All rights reserved.
Contents
■CHAPTER1Introduction to Genexus™ Software ............................... 13
Software overview ............................................................. 13
Software compatibility and requirements .......................................... 13
Softwareanomalies ........................................................ 14
Network and password security requirements ..................................... 14
Network configuration andsecurity .......................................... 14
Passwordsecurity ......................................................... 14
Installation and verificationrun ................................................... 14
■CHAPTER2Get started with Genexus™ Software ............................. 15
About Genexus™ Software ...................................................... 16
Access the End User License Agreement(EULA) .............................. 17
Contact Support ........................................................... 17
User-accesslevels ............................................................. 17
System tracking ............................................................... 18
Reagentmanagement .......................................................... 18
Viewnotifications .............................................................. 19
Request and sign in to a new useraccount ........................................ 19
Signin ........................................................................ 20
Edit a userprofile .............................................................. 20
Genexus™ Softwareconcepts ................................................... 21
Workflows .................................................................... 21
Sample to Resultworkflow ................................................. 22
Nucleic Acid to Result or Library to Resultworkflow .......................... 24
Bam to Resultworkflow .................................................... 26
■CHAPTER3Samples and librarybatches ...................................... 27
About samples and librarybatches ............................................... 27
Enter and managesamples ..................................................... 27
Customize the samplestable ................................................ 28
Findsamples .............................................................. 28
Create a newsample ....................................................... 33
Create multiplesamples .................................................... 33
Genexus™ Software 6.8 User Guide 3
Importsamples ............................................................ 34
Upload a BAM file to create a sample orsamples .............................. 35
View sample summary ..................................................... 37
Download a template file for sample creation .................................. 38
Sample attributes (manager/administrator) .................................... 39
Sampletags .............................................................. 46
Managesamples .......................................................... 49
Enter and manage librarybatches ................................................ 54
Prepare or import a librarybatch ............................................. 54
Find librarybatches ........................................................ 57
Manage librarybatches ..................................................... 60
■CHAPTER4Plan and manage runs ............................................. 62
Before you plan arun ........................................................... 63
Find a runplan ................................................................. 63
Search for a runplan ....................................................... 64
Sort the list of runplans .................................................... 65
Filter the list of runplans .................................................... 65
Integrated nucleic acid isolation in Sample to Resultruns ........................... 66
Plan a Sample to Resultrun ................................................ 66
Review samples for Sample to Resultruns .................................... 71
Abort a Sample to Resultrun ................................................ 71
Plan a Nucleic Acid to Resultrun ................................................ 72
Plan a Library to Resultrun ..................................................... 76
Plan a BAM to Result run ....................................................... 80
Find the assay that you want to use in a runplan ................................... 81
Search for an assay to use in a runplan ...................................... 81
Filter the list of assays shown when you plan arun ............................. 82
Manageruns .................................................................. 83
View a runplan ............................................................ 83
Print a runplan ............................................................ 85
Review and download a run history .......................................... 85
Edit arun ................................................................. 86
Delete arun ............................................................... 86
Add a note to arun ........................................................ 87
■CHAPTER5Genexus™ Software Dashboard ................................... 88
View run progress on theinstrument .............................................. 90
Filter the list of samples shown in the dashboard .............................. 92
View the status of aninstrument ................................................. 92
Information about connected instruments on the Dashboard ........................ 93
Contents
4Genexus™ Software 6.8 User Guide
■CHAPTER6Review data and results ............................................ 94
Results navigation bar overview ................................................. 94
Review sample results .......................................................... 96
View sequencing results .................................................... 98
View keyfindings .......................................................... 98
The Key Variantsmatrix ................................................... 100
View the amplicon coverage ............................................... 102
View variant results ....................................................... 103
Review the variant pileupview ............................................. 127
View more annotations and annotation sources .............................. 133
View the QC results ....................................................... 133
Sample tags in sample results .............................................. 138
Customize the sample resultstable ......................................... 139
Find sample results ....................................................... 140
Review run results ............................................................ 144
View the run summary .................................................... 146
View assay metrics and the run report ....................................... 150
Retain run results ......................................................... 155
Release run results ....................................................... 156
Assign PCR Plate ......................................................... 156
Find a run result .......................................................... 157
Compare sample results ....................................................... 161
Compare variant results ................................................... 161
Compare immune repertoire results ......................................... 167
Resultsfiles .................................................................. 171
Download results files for multiple sample results ............................. 174
Download results files for a sample result .................................... 175
Results from some system-installedassays ...................................... 175
Microbiome assay results .................................................. 175
View Oncomine™ TCR Beta‑LRAssayGX results ............................. 188
View verification run results .................................................... 189
Verificationruns .......................................................... 190
Sign verification run reports (manager/administrator) .......................... 190
Run plugins after a sequencing run is complete ................................... 191
Reanalysis ................................................................... 192
Reanalyze arun .......................................................... 192
Reanalyze asample ....................................................... 194
Upload results to another softwareaccount ...................................... 195
Upload results files to another Genexus™ IntegratedSequencer ................ 195
Upload results files to Ion Reporter™ Software ................................ 196
Data files andflow ............................................................ 197
Contents
Genexus™ Software 6.8 User Guide 5
■CHAPTER7Create, view, and sign reports ................................... 198
Variant report ................................................................. 198
View a variant report ...................................................... 199
Download a variant report ................................................. 200
Generate a variant report .................................................. 200
Delete a variant report ..................................................... 201
Sign o variant reports .................................................... 201
Send a notification to anotheruser .......................................... 203
Report templates (manager/administrator) ....................................... 203
Preview a report template (manager/administrator) ............................ 203
Create a report template (manager/administrator) ............................. 205
Edit a draft report template (manager/administrator) ........................... 210
Delete a draft report template (manager/administrator) ........................ 210
Lock a draft report template (manager/administrator) .......................... 211
View or add notes to a report template (manager/administrator) ................ 211
Configure electronic signatures (administrator) ................................... 211
Manage electronic signature types (administrator) ............................ 212
Run report ................................................................... 214
View a run report ......................................................... 214
Download a run report .................................................... 214
■CHAPTER8Create and manage assays (manager/administrator) .......... 215
Assays in Genexus™ Software .................................................. 215
Find anassay ................................................................ 216
Search forassays ........................................................ 216
Sort the list ofassays ..................................................... 217
Filter and search in the list ofassays ........................................ 217
Assay creation overview ....................................................... 218
Create an assay (manager/administrator) .................................... 219
Copy an assay (manager/administrator) ..................................... 221
Assayoptions ............................................................ 222
Custom assays for Sample to Result runs (manager/administrator) ............. 234
Manageassays ............................................................... 236
View assaydetails ........................................................ 236
Import an assay (manager/administrator) .................................... 238
Export a custom, locked assay (manager/administrator) ....................... 238
Review and export an assay history ......................................... 238
Edit a draft assay (manager/administrator) ................................... 239
Lock a draft assay (manager/administrator) .................................. 240
Delete a draft assay (manager/administrator) ................................. 240
Edit the QC parameters of a locked assay (manager/administrator) ............. 241
Use the latest annotation source (manager/administrator) ...................... 241
Use a fixed version of an annotation source (manager/administrator) ............ 242
Contents
6Genexus™ Software 6.8 User Guide
Remove access to an assay (manager/administrator) .......................... 242
Download assay parameters ............................................... 242
Gene lists (manager/administrator) .............................................. 243
View a gene list (manager/administrator) ..................................... 243
Create a gene list (manager/administrator) ................................... 244
Edit a gene list (manager/administrator) ..................................... 245
Change the default gene list (manager/administrator) .......................... 246
Delete a gene list (manager/administrator) ................................... 246
Lock a gene list (manager/administrator) ..................................... 247
Remove a gene list (manager/administrator) .................................. 247
Review a gene list history (manager/administrator) ............................ 247
■CHAPTER9Presets and panels (manager/administrator) .................... 249
Annotation sets(manager/ administrator) ......................................... 249
View annotation setdetails ................................................ 250
Create a new annotation set (manager/administrator) ......................... 250
Make custom annotation setsunavailable ................................... 253
Updated versions ofannotations ........................................... 254
Filters and filterchains ......................................................... 255
Review filter chaindetails .................................................. 256
Create a custom filter chain (manager/ administrator) ......................... 256
Create a custom filter chain with groups (manager/ administrator) .............. 258
Copy a filter chain (manager/administrator) .................................. 259
Edit a filter chain (manager/administrator) .................................... 260
Delete a filter chain (manager/administrator) .................................. 260
Lock a filter chain (manager/administrator) ................................... 261
Obsolete a custom filterchain .............................................. 261
Review and export a filter chain history(manager/ administrator) ................ 261
Custom filter chain examples (manager/administrator) ......................... 263
Copy number baselines(manager/ administrator) .................................. 265
View copy number baseline details (manager/administrator) .................... 266
Create a copy number baseline (manager/administrator) ....................... 267
Augment a copy number baseline with more samples (manager/administrator) ... 269
Copy a copy number baseline (manager/administrator) ........................ 270
View, add, or remove a note in a copy number baseline(manager/ administrator) . 271
Import a copy number baseline (manager/administrator) ....................... 271
Download the log files for copy number baseline
creation (manager/administrator) ......................................... 272
Delete a copy number baseline (manager/administrator) ....................... 272
Export a custom copy number baseline (manager/administrator) ................ 273
Remove a copy number baseline (manager/administrator) ..................... 273
Sequence variantbaselines .................................................... 274
View sequence variant baseline details (manager/administrator) ................ 274
Create a sequence variant baseline (manager/administrator) ................... 275
Copy a sequence variant baseline (manager/administrator) .................... 276
Contents
Genexus™ Software 6.8 User Guide 7
Import a sequence variant baseline (manager/administrator) ................... 276
View, add, or remove a note in a sequence variant baseline(manager/
administrator) .......................................................... 278
Download the log files for sequence variant baseline
creation (manager/administrator) ......................................... 278
Delete a sequence variant baseline (manager/administrator) ................... 279
Export a custom sequence variant baseline (manager/administrator) ............ 279
Remove a sequence variant baseline (manager/administrator) .................. 279
Exon tile assaybaselines ...................................................... 280
View exon tile assay baseline details (manager/administrator) .................. 280
Create an exon tile assay baseline (manager/administrator) .................... 281
View, add, or remove a note in an exon tile assay baseline(manager/
administrator) .......................................................... 283
Import an exon tile assay baseline (manager/administrator) .................... 284
Download the log file for custom exon tile assay
baselines (manager/administrator) ........................................ 284
Delete an exon tile assay baseline (manager/administrator) .................... 285
Export an exon tile assay baseline (manager/administrator) .................... 285
Remove an exon tile assay baseline (manager/administrator) ................... 285
Panel files (manager/administrator) .............................................. 286
Manage panels (manager/administrator) ..................................... 286
Manage hotspot files (manager/administrator) .................................... 289
View hotspot filedetails ................................................... 289
Add new hotspot files(manager/ administrator) ............................... 290
Export hotspot files(manager/ administrator) ................................. 290
Obsolete hotspot files(manager/ administrator) ............................... 290
Reactivate hotspot files(manager/ administrator) ............................. 291
Manage fusion reference files (manager/administrator) ............................ 291
View fusion reference filedetails ............................................ 291
Add fusion reference files(manager/ administrator) ............................ 292
Export fusion reference files(manager/ administrator) .......................... 292
Obsolete fusion reference files(manager/ administrator) ....................... 292
Reactivate fusion reference files(manager/ administrator) ...................... 293
Manage reference genome files (manager/administrator) .......................... 293
View reference genome filedetails .......................................... 293
Add reference genome files(manager/ administrator) .......................... 293
Obsolete reference genomes(manager/ administrator) ......................... 294
Reactivate reference genomes(manager/ administrator) ....................... 294
Manage barcode sets (manager/administrator) ................................... 295
View barcode set details (manager/administrator) ............................. 295
Add new barcodesets (manager/ administrator) .............................. 295
Obsolete barcode sets(manager/ administrator) .............................. 296
Control fragments (manager/administrator) ....................................... 296
Contents
8Genexus™ Software 6.8 User Guide
■CHAPTER10System administration and
management (manager/administrator) ......................................... 297
Linked accounts in Genexus™ Software (manager/administrator) .................... 298
Create a Connectaccount ................................................. 298
Configure a Thermo Fisher™ Connect Platform account with a QR
code (manager/administrator) ............................................ 299
Register Genexus™ Software accounts (manager/administrator) ................ 300
Register an Ion Reporter™ Software on Thermo Fisher™ Connect Platform
account (manager/administrator) ......................................... 300
Register an Ion Reporter™ Server account (manager/administrator) ............. 301
Manage connectedaccounts .............................................. 302
User accounts (administrator) .................................................. 304
Add a new user account (administrator) ..................................... 304
Sort the user list(admin) ................................................... 305
Edit user details (administrator) ............................................. 305
Reset user password ...................................................... 305
View user account history (administrator) .................................... 306
Set user account security policies (administrator) ............................. 307
Configure an SSH key (system administrator) ................................ 307
Audit records (administrator) ................................................... 308
Search audit records (administrator) ......................................... 308
Sort audit records (administrator) ........................................... 309
Export audit records (administrator) ......................................... 309
Update the audit configuration (administrator) ................................ 310
Configure email settings (manager/administrator) ................................. 310
Configure email notifications (manager/administrator) ......................... 310
Labinformation .......................................................... 311
Software updates ............................................................. 312
Available versions of software updatepackages .............................. 312
Download and install software from the App Store (administrator) .............. 313
Format a USB drive for a software update ................................... 314
Download and install software with a USB drive (administrator) ................. 314
Manage backup settings and restore runs (administrator) .......................... 315
Disk space usage and backup settings (administrator) ......................... 316
Configure backup settings (administrator) .................................... 319
Archive a run result (administrator) .......................................... 328
Delete a run result (administrator) ........................................... 329
Data output directory ..................................................... 330
Emailnotifications ........................................................ 330
Restore run results (administrator) .......................................... 331
Contents
Genexus™ Software 6.8 User Guide 9
Log files (administrator) ........................................................ 334
View log files (administrator) ............................................... 334
Manage log settings (administrator) ......................................... 335
View the log settings history ............................................... 335
System services (manager/administrator) ........................................ 335
Terminate an active job(manager/ administrator) .............................. 336
Start a stopped service(manager/ administrator) .............................. 336
Disable or enable the Smart Monitoring service(manager/ administrator) ......... 337
■CHAPTER11Plugins for dataanalysis ........................................ 338
coverageAnalysis plugin in Genexus™ Software ................................... 338
Review coverageAnalysis plugin results ..................................... 338
Readsstatistics .......................................................... 339
Example charts generated by the coverageAnalysisplugin ..................... 342
Example Coverage Analysis Report ........................................ 345
Output files generated by the coverageAnalysisplugin ........................ 346
molecular Coverage Analysis plugin in Genexus™ Software ......................... 348
Review molecular Coverage Analysis plugin results ............................ 349
Moleculestatistics ........................................................ 350
Example Molecular Coverage Analysis Report .............................. 351
Example charts generated by the molecular Coverage Analysisplugin ........... 351
Output files generated by the molecular Coverage Analysisplugin ............... 353
IonReporterUploaderplugin .................................................... 355
Review IonReporterUploader plugin results .................................. 356
Customer Support Archive ..................................................... 357
sampleIDplugin .............................................................. 357
Review sampleID plugin results in Genexus™ Software ........................ 357
■APPENDIXAGenexus™ Software web servicesAPI ......................... 360
LIMS introduction ............................................................. 360
LIMS system FTP setup or drivemapping ................................... 362
API common parameters ....................................................... 363
Get list of Ion Reporter™ Softwareaccounts ...................................... 364
Get assaylist ................................................................. 365
Getsamples ................................................................. 366
Get librarybatches ............................................................ 366
Get runplans ................................................................. 368
Get report templates .......................................................... 369
Get results ................................................................... 369
Get signed osamples ........................................................ 375
Download files for completedruns .............................................. 376
Createsamples ............................................................... 377
Contents
10 Genexus™ Software 6.8 User Guide
Create a librarybatch .......................................................... 379
Create a Sample to Result (purification)run ...................................... 380
Create a Nucleic Acid to Resultrun ............................................. 381
Create a libraryrun ............................................................ 381
■APPENDIXBReferenceinformation ........................................... 383
Rules for variant names in Genexus™ Software ................................... 383
Annotation criteria for Oncomine™ Variant Annotator .............................. 385
Oncomine™ BRCA Assay GX  .............................................. 386
Oncomine™ Comprehensive Assay v3GX .................................... 386
Oncomine™ Myeloid Assay GXv2 .......................................... 389
Oncomine™ Precision AssayGX ............................................ 392
Custom panelassay ...................................................... 395
Ion Torrent™ Class-Based Variants .......................................... 399
Variant identifiers for Oncomine™panels ......................................... 402
System-installed annotationsets ................................................ 403
System-installed barcodesets .................................................. 404
System-installed filterchains ................................................... 405
System-installedfilters ........................................................ 406
Filters for genes andvariants ............................................... 407
Filters for population frequencies ........................................... 410
Filters formetrics ......................................................... 412
Annotation sourcefilters ................................................... 415
Filters for functional scores ................................................ 418
Otherfilters .............................................................. 419
System-installedplugins ....................................................... 423
System-installed reference genomefiles ......................................... 423
System-installed report templates ............................................... 424
System-installed sample attributes ............................................. 424
System-installed verification templates .......................................... 426
■APPENDIXCTroubleshooting .................................................. 427
Download InstrumentDiagnostics ............................................... 427
Customer Support Archive(CSA) ............................................... 428
Download a Customer Support Archive ..................................... 428
Troubleshoot Genexus™ Software .............................................. 428
Contents
Genexus™ Software 6.8 User Guide 11
■APPENDIXDDocumentation and support .................................... 431
Relateddocumentation ........................................................ 431
Customer and technical support ................................................ 431
Limited product warranty ...................................................... 432
Glossary ................................................................................. 433
Contents
12 Genexus™ Software 6.8 User Guide
Introduction to Genexus™ Software
■ Software overview .................................................................... 13
■ Software compatibility and requirements ................................................ 13
■ Network and password security requirements ............................................ 14
■ Installation and verificationrun ......................................................... 14
Software overview
Ion Torrent™ Genexus™ Software supports the Ion Torrent™ Genexus™ Integrated Sequencer workflow
for research use purposes from sample preparation through library preparation, template preparation,
and sequencing. During and after sequencing, the software generates base calls, trims reads, and
determines quality values (primary analysis), then aligns reads, calls variants, and generates reports
(secondary analysis). The software also supports the Ion Torrent™ Genexus™ Purification System for
nucleic acid isolation, followed by sequencing on the Genexus™ Integrated Sequencer.
This documentation provides instructions for using the software to perform the following functions:
•Create and manage samples, libraries, assays, and runs in the software.
•Monitor the status of runs on the Genexus™ Purification System and the Genexus™ Integrated
Sequencer, which provides all-in-one library preparation, chip loading, template preparation, and
sequencing.
•View data, results, and quality control (QC) reports after a run.
•Download data files.
•Export and print audit records.
•Create and manage annotation sets, genome references, report templates, baseline files, primer
sets, plugins, and reference files.
•Create and manage user accounts.
Software compatibility and requirements
The procedures in this guide are designed for use with Genexus™ Software6.8 or later. Version-specific
information is provided in the software release notes for each version of the software. An administrator-
level user can view the software version in the (Settings) / Software Updates screen.
Genexus™ Software is supported on Google Chrome™ browser version 90 and later and is best
viewed with 1440 × 900 screen resolution. Google Chrome™ browser is recommended for use with
the software.
The operating system of the sequencer is Ubuntu™ 18.04.1 LTS.
1
Genexus™ Software 6.8 User Guide 13
Software anomalies
For Genexus™ Software anomalies, see the release notes for your version of the software. You can also
download the release notes, as well as the Genexus™ Software 6.8 User Guide (Pub. No. MAN0026409),
at http://www.thermofisher.com/ngssoftwaresupport.
Network and password security requirements
Network configuration and security
The network configuration and security settings (for example, firewalls, antivirus software, network
passwords) of your laboratory or facility are the sole responsibility of your facility administrators and
IT and security personnel. Genexus™ Software does not provide any network or security configuration
files, utilities, or instructions.
If external or network drives are connected to the sequencer, it is the responsibility of your IT personnel
to ensure that such drives are configured and secured correctly to prevent data corruption or loss.
If a LIMS connection is set up, you can use the LIMS API to get the list of files generated for the assay.
For more information, see “LIMS introduction” on page360.
Note: If a LIMS system is configured to retrieve files from the sequencer, you have the option to
manually set up an FTP directory or drive mapping. This configuration is not provided as part of
sequencer installation, and must be set up by your LIMS system integration or IT group.
Password security
Best practice is to maintain unique passwords for all accounts in use in Genexus™ Software. All
passwords must be reset the first time a user signs into the software. Change passwords according to
your organization's password policy.
It is the sole responsibility of your IT personnel to develop and enforce secure use of passwords.
This feature allows you to meet Title 21 CFR Part 11 of Federal Regulations that establishes the
United States Food and Drug Administration regulations on electronic records and signatures, password
policies, and user activity auditing.
Installation and verification run
IMPORTANT! The Genexus™ Integrated Sequencer and the Genexus™ Software provides the option to
perform a performance qualification verification run.
Notifications are sent when the PQ run is expired. Contact your Field Support Engineer (FSE) or
Technical Support if you have questions about an expired PQ status.
Chapter1Introduction to Genexus™ Software
Network and password security requirements
1
14 Genexus™ Software 6.8 User Guide
Get started with Genexus™ Software
■ About Genexus™ Software ............................................................ 16
■ User-accesslevels ................................................................... 17
■ System tracking ...................................................................... 18
■ Reagentmanagement ................................................................. 18
■ Viewnotifications ..................................................................... 19
■ Request and sign in to a new useraccount .............................................. 19
■ Signin .............................................................................. 20
■ Edit a userprofile ..................................................................... 20
■ Genexus™ Softwareconcepts ......................................................... 21
■ Workflows ........................................................................... 21
2
Genexus™ Software 6.8 User Guide 15
About Genexus™ Software
Genexus™ Software provides menus to help you add, select, and manage samples, libraries, runs, and
assays. You can also view and manage sequencing results, monitor Genexus™ Integrated Sequencer
runs in progress, and manage software settings.
1 3 4 5 6 7 82
1Dashboard—View recent run history, and current purification or sequencing run status.
2Samples—Add new samples, import samples, prepare library batches, import library batches and manage attributes.
3Runs—Plan a run starting from a sample, a nucleic acid sample, a BAM sample, or a library. View, edit, and manage runs.
Sample to result runs are for nucleic acid isolation on a Genexus™ Purification Instrument followed by sequencing on a
Genexus™ Integrated Sequencer.
4Results—View sample results, run results, and verification results.
5Assays—Manage, create, and import assays. Manage assay preset parameters and panels.
6Notifications—Receive alerts and messages for password expiration, system critical service failures, system backup failures,
available software updates, and full disk space.
7Settings—Access audit records and run logs, configure network settings, manage backup settings, restore runs, manage
gene lists, link to Connect user accounts and Ion Reporter™ Software accounts, check for software updates, and manage data
archiving, disk space, and users. Field Service Engineers access verification templates during sequencer installation.
8Profile—Access the Help system, manage and edit user profile settings, configure an SSH key (system administrator only),
and sign out.
Chapter2Get started with Genexus™ Software
About Genexus™ Software
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16 Genexus™ Software 6.8 User Guide
Access the End User License Agreement (EULA)
A link to the End User License Agreement (EULA) is located at the bottom of the screen.
1. Scroll to the bottom of the screen.
2. Click the EULA link to open a PDF file of the EULA.
Contact Support
You can access Genexus™ Software technical support from the software.
1. Scroll to the bottom of the screen.
2. Click Support to open https://www.thermofisher.com/contactus, where you can request help
and technical support.
User-access levels
Users at this level Can perform these actions
Report •Access the Sample Results and Run Results screens to view results
•Generate, view, and sign variant reports
•Send notifications
•Download results files
•View and edit notes for the sample result
•View the audit trail for sample results
•View notifications
Operator Report functions, plus:
•Add, import, and export sample files
•Edit sample files
•Prepare library batches
•Plan, save, audit, and delete runs
•Monitor runs
•View results and reports
•Upload sample results files to Ion Reporter™ Software
•View the audit trail for samples, library batches, runs, and assays
•Reanalyze runs and run plugins
Chapter2Get started with Genexus™ Software
User-access levels 2
Genexus™ Software 6.8 User Guide 17
(continued)
Users at this level Can perform these actions
Manager Operator functions, plus:
•Create, edit, and obsolete sample attributes
•Create and import assays
•Create presets for annotation sets, filter chains, copy number baselines,
sequence variant baselines, exon tile assay baselines, and report templates
•Edit and delete sample files
•Add or edit Thermo Fisher accounts
•Manage gene lists
•Restart a stalled or failed run
•Manage reference sequences and panel, hotspot, and other sequence files
•Access services information
Administrator Operator and manager functions, plus:
•View, export, and print audit records
•Configure network settings
•View and manage software updates
•Install and manage plugins
•Configure backup settings and restore runs
•Manage sequencer and software log files
•Add and manage user accounts
System tracking
The system tracks and checks auditable user activities for samples, assays, QC metrics and information
related to reagents.
If the software detects an error at any step—for example, a scanned barcode is inconsistent with the
information given for the run—the software alerts the user and does not proceed with the run.
This feature allows you to meet Title 21 CFR Part 11 of Federal Regulations that establishes the
United States Food and Drug Administration regulations on electronic records and signatures, password
policies, and user activity auditing.
Reagent management
Put in place a reagent management system to inventory and track reagent use.
Proper use of a reagent management system ensures optimal use of kits, chips, and reagents.
Chapter2Get started with Genexus™ Software
System tracking
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18 Genexus™ Software 6.8 User Guide
View notifications
You can view notifications for files that you upload and import in Genexus™ Software.
1. In the menu bar, click (Notifications).
If you have any unread notifications, the number of unread notifications is shown to the upper right
of the notification button.
2. View the list of notifications in the dialog box that appears.
3. To delete a notification, click (Remove) in the section of the notification.
Request and sign in to a new user account
Operator-level users must request a new user account from the manager- or administrator-level user
before they can sign in to Genexus™ Software.
Administrator-level users receive the request and create the user account.
Your user name and password must be unique and not shared with other users.
•To request a new account, contact your administrator-level user.
After the administrator creates a new account, the software sends an email to the new user with a
user name and temporary password.
•To sign in to a new account for the first time:
a. Obtain your user name and temporary password that is supplied by your administrator in an
email message.
b. Browse to the Genexus™ Software sign in page (for example, https://<your server address>)
enter your user name and the temporary password supplied by your administrator.
c. Press Enter, or click Sign In.
d. In the End User License Agreement that appears at first sign on, read the agreement, then
click Accept.
e. In the Change Password screen, enter your temporary password supplied by your
administrator.
f. Type a new password, confirm the password, then click Change.
–Passwords must be between 8 and 80 characters.
–Passwords must contain only alphanumeric characters (numbers 0 to 9 and letters A to Z),
no spaces or special characters.
–Passwords must contain at least one alphabetic character (a–z, A–Z).
–Passwords must contain at least one numeric character (0–9).
–Passwords are case-sensitive.
Chapter2Get started with Genexus™ Software
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Genexus™ Software 6.8 User Guide 19
Genexus™ Software opens to the Dashboard screen.
Sign in
Before you can sign in to Genexus™ Software, you must have a registered account. For more
information, see “Request and sign in to a new user account” on page19.
1. Go to the Genexus™ Software sign in page.
2. Click Switch Language, then select the preferred language from the dropdown list that appears, if
desired.
3. Enter your user name and password, then press Enter or click Sign In.
Note: If a message appears that indicates that there is a problem with the security token, refresh
the browser and enter the user name and password again.
The software opens to the Dashboard screen.
Edit a user profile
After your user profile has been established, you can view user profile information, change a password,
or change email contact information.
1. In the menu bar, click (Profile)4MyProfile.
2. In the Profile screen, view the profile information.
To Do this
Change a password 1. Click Change Password.
2. In the Change Password dialog box, enter the current password and
a new password. Confirm the password, then click Change.
Change an email address 1. Click Change Email.
2. In the Set Email dialog box, enter a new email address, and a
password, then click Save.
Edit security questions
and answers 1. Click Edit Security questions and answers.
2. In the Edit Security questions and answers dialog box, select a
security question from the dropdown list, then enter an answer.
3. Enter the password for the account that is associated with the profile.
4. Click Submit.
The changes are applied immediately. After the password is changed, you must sign in with the new
password.
Chapter2Get started with Genexus™ Software
Sign in
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20 Genexus™ Software 6.8 User Guide
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