Thermo Fisher Scientific Genexus Software 6.8 User guide

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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registered trademarks of Microsoft Corporation. Apache and OpenOce are registered trademarks of The Apache Software Foundation.

Amazon Web Services is a trademark of Amazon.com, Inc. or its aliates in the United States and/or other countries.

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 Resultworkﬂow ................................................. 22

Nucleic Acid to Result or Library to Resultworkﬂow .......................... 24

Bam to Resultworkﬂow .................................................... 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

2

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

2

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

View notiﬁcations 2

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

2

20 Genexus™ Software 6.8 User Guide

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Thermo Fisher Scientific Genexus Software 6.8 User guide

Thermo Fisher Scientific Genexus Software 6.8 User guide

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