Thermo Scientific Ion Torrent S5 User manual

USER GUIDE
For Research Use Only. Not for use in diagnostic procedures.
CONFIDENTIAL — For Life Technologies Internal Use Only. Do Not Distribute.
Ion Torrent S5™and Ion Torrent S5™XL
Sequencer
Catalog Numbers A27211, A27213
Publication Number MAN0010811
Revision A.0

The information in this guide is subject to change without notice.
DISCLAIMER
LIFE TECHNOLOGIES CORPORATION AND/OR ITS AFFILIATE(S) DISCLAIM ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT, EXPRESSED OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NON-INFRINGEMENT. TO
THE EXTENT ALLOWED BY LAW, IN NO EVENT SHALL LIFE TECHNOLOGIES AND/OR ITS AFFILIATE(S) BE LIABLE, WHETHER IN CONTRACT, TORT,
WARRANTY, OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE OR CONSEQUENTIAL
DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING BUT NOT LIMITED TO THE USE THEREOF.
Important Licensing Information
These products may be covered by one or more Limited Use Label Licenses. By use of these products, 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.
©2015 Thermo Fisher Scientific Inc. All rights reserved.

Contents
About this guide ............................................................ 5
Revision history ................................................................. 5
Purpose of the guide ............................................................ 5
■CHAPTER 1 Product information ....................................... 6
Contents ....................................................................... 6
Required materials and equipment ................................................ 7
Update the software ............................................................. 8
Instrument installation by trained personnel only ................................... 8
Nucleic acid contamination ....................................................... 8
Instrument vibration and clearances .............................................. 8
Static electricity ................................................................ 8
■CHAPTER 2 System components ....................................... 9
Internet connectivity ............................................................ 10
Ion Torrent S5™System component positions ...................................... 11
Ion Torrent S5™and Ion Torrent S5™XL Sequencer input and output connections ...... 12
■CHAPTER 3 Create a Planned Run .................................... 13
About planned runs ............................................................ 13
Create a planned run ........................................................... 13
Planned run wizard: key fields ................................................... 14
■CHAPTER 4 Instrument operation .................................... 16
Power the Ion Torrent S5™or Ion Torrent S5™XL Sequencer on or off ................. 16
Power on ................................................................. 16
Power off ................................................................. 16
Chip handling guidelines ........................................................ 16
Select the planned run and perform the run ....................................... 17
Update the Ion Torrent S5™System software ...................................... 18
Clean the instrument ........................................................... 19
Ion Torrent S5™andIon Torrent S5™XL Instrument User Guide
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■APPENDIX A Touchscreen reference ................................. 20
Clean, Initialize, and Run ........................................................ 20
Options and Tools .............................................................. 21
Touchscreen gauges ........................................................... 22
Chip status icon ................................................................ 23
Alarms/events pop-up .......................................................... 23
■APPENDIX B Troubleshooting ......................................... 26
Ion Torrent S5™Sequencer alarms and events ..................................... 26
Chip Check .................................................................... 27
Chip calibration (before loading sample) .......................................... 28
Chip calibration (after loading sample) ........................................... 29
Initialization—General errors ................................................... 30
Troubleshooting using the controls ............................................... 30
■APPENDIX C Supplemental procedures .............................. 31
Set up and test the Ion Chip™Minifuge ............................................ 31
Install the Ion Proton™Rotor and Buckets ..................................... 31
Test the minifuge .......................................................... 32
■APPENDIX D Safety ..................................................... 34
Symbols on this instrument ..................................................... 34
Conformity symbols on this instrument ....................................... 35
Safety alerts on this instrument .................................................. 36
Location of safety labels on this instrument ................................... 36
Safety information for instruments not manufactured by Thermo Fisher Scientific ..... 37
Instrument safety .............................................................. 37
General .................................................................. 37
Electrical ................................................................. 37
Cleaning and decontamination .............................................. 38
Safety and electromagnetic compatibility (EMC) standards .......................... 39
Safety .................................................................... 39
EMC ...................................................................... 39
Environmental design ...................................................... 39
Chemical safety ................................................................ 41
■Documentation and support ............................................. 43
Placeholder for related documentation ........................................... 43
Customer and technical support ................................................. 43
Limited product warranty ....................................................... 43
Contents
4 Ion Torrent S5™andIon Torrent S5™XL Instrument User Guide
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About this guide
CAUTION! ABBREVIATED SAFETY ALERTS. Hazard symbols and hazard
types specified in procedures may be abbreviated in this document. For the
complete safety information, see the “Safety” appendix in this document.
IMPORTANT! Before using this product, read and understand the information in the
“Safety” appendix in this document.
Revision history
Revision Date Description
A.0 November 2014 Ion Torrent S5
™and Ion Torrent S5 ™XL Instrument
User Guide for compliance testing.
Purpose of the guide
The Ion Torrent S5™ and Ion Torrent S5™ XL Instrument User Guide (Pub. no.
MAN0010811) provides reference information for using the
Ion Torrent S5™ or Ion Torrent S5™ XL Sequencer's (Cat. nos. A27211 and A27213).
Ion Torrent S5™andIon Torrent S5™XL Instrument User Guide
5
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Product information
Contents
The Ion Torrent S5™ and Ion Torrent S5™ XL Systems (Catalog nos. A27212, or
A27214) contain the following boxes and components.
Ion Torrent S5™System (Catalog no. A27212)
Components Catalog no.
Ion Torrent S5™Sequencer A27211
Ion S5™Installation Kit A27215
Ion Torrent S5™XL System (Catalog no. A27214)
Components Catalog no.
Ion Torrent S5™XL Sequencer A27213
Ion S5™Installation Kit A27215
Ion S5™Installation Kit (Catalog no. A27215)
Components Color Quantity Volume Storage
Ion 520™& 530™OT2 Kit — 4 — 2°C to 8°C
Ion 540™Chip Kit — 4 — 15°C to 30°C
Ion Torrent S5™Sequencing Kit — 4 — 2°C to 8°C
Ion S5™Controls Kit — 1 — 2°C to 8°C
1
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Required materials and equipment
The following tables list required materials and equipment that are not provided with
the Ion Torrent S5™ Systems.
Table 1 Required materials and equipment for sequencing
3Description[1] Supplier Catalog no. Quantity
Ion Chip™Minifuge (120 V or 230 V) Life
Technologies 4479672 (120V) or
4479673 (230V)
1
Ion Proton™Rotor and Buckets Kit Life
Technologies 4482578 1
Uninterruptable Power Supply (UPS) [2] MLS — 1
Isopropanol (100%) MLS — —
Nuclease-free water molecular biology grade MLS — —
Microcentrifuge[3] MLS — 1
P2, P10, P20, P200, P1000 µL pipette set and filtered tips MLS — 1 set
Rainin®Pipet-Lite®XLS with RFID LTS 2 µL to 20 µL Rainin L-20XLS 1
Rainin®Pipet-Lite®XLS with RFID LTS 10 µL to 100 µL Rainin L-100XLS 1
Rainin®StableRak™LTS tips 2-20 µL Rainin SR-L20F —
Rainin®StableRak™LTS tips 200 µL Rainin SR-L200F —
0.2-mL MAXYMum Recovery®Thin Wall PCR Tubes, Flat
Cap (do not use polystyrene tubes) Axygen PCR-02-L-C Varies
1.5-mL or 1.7-mL microcentrifuge tubes MLS — Varies
Ice buckets and ice — — —
Aluminum heat block, capable of maintaining 50°C MLS — —
Vortex mixer with a rubber platform MLS — 1
Thermal cycler with a heated lid MLS — 1
Standard laboratory vacuum line or vacuum pump MLS — 1
Liquid trap MLS — 1
Tygon®tubing [4] MLS — 1
[1] Thermo Fisher Scientific has validated this protocol using these specific materials. Substitution may adversely affect system performance.
[2] For laboratories that experience frequent power outages or line voltage fluctuations, we recommend that you use an uninterruptable power
supply that is compatible with 2500 W output or higher.
[3] Must fit standard 1.5- and 0.2-mL microcentrifuge tubes and generate 15,500 ×
g .
[4] As needed to connect laboratory vacuum to liquid trap and liquid trap to P200 pipette tip.
Chapter 1 Product information
Required materials and equipment
1
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Update the software
IMPORTANT! Before proceeding, make sure that you have updated the Torrent
Suite™ and Ion Torrent S5™ System software to Version 4.4 or later. See “Update the
Ion Torrent S5™ System software“ on page 18.
Instrument installation by trained personnel only
IMPORTANT! The Ion Torrent S5™ System is installed by trained service personnel
and must not be relocated without assistance from trained service personnel. See
“Customer and technical support“ on page 43.
Nucleic acid contamination
IMPORTANT! A primary source of contamination is DNA fragments from previously
processed samples. Do not introduce amplified DNA into the library preparation
laboratory or work area.
Instrument vibration and clearances
IMPORTANT! Significant vibration during sequencing may add noise and reduce the
quality of the measurements. The Ion Torrent S5™ System must be installed on a
bench that is free from vibrations or in contact with equipment that can cause
vibrations to the bench (freezers, pumps, and other similar equipment).
IMPORTANT! Place the instrument at least 40 in. (1 meter) away from major sources
of electronic noise such as refrigerators or microwaves.
Static electricity
IMPORTANT! To avoid possible damage to the chip from static electricity, you must
ground yourself on the grounding plate (located next to the chip clamp) prior to
handling chips, and do not place chips on non-grounded surfaces such as a bench.
Always use the grounding plate to hold chips that are not in the package or inserted
in the chip clamp or the Ion PGM™ Chip Minifuge bucket.
Chapter 1 Product information
Update the software
1
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System components
We support the layout in which the Ion Torrent™ Server is directly connected to the
Ion Torrent S5™ XL Sequencer, rather than through the local area network from a
remote location such as a server room. Data are most robustly transferred from the
Ion Torrent S5™ XL Sequencer to the Ion Torrent™ Server when they are directly
connected by a standard Category 6 Ethernet cable provided with the installation
materials.
IMPORTANT! The Ion Torrent S5™ System must be connected to the Ion Torrent™
Server by a standard Category 6 Ethernet cable. We do not troubleshoot data transfer
issues associated with an indirect connection between the Ion Torrent S5™ XL
Sequencer and the Ion Torrent™ Server.
Torrent Browser
3
4
5
6
2
1
Figure 1 Ion Torrent S5™XL Sequencer configuration
1Ion Torrent S5™XL Sequencer
2Ion template preparation instrument (Ion
Chef™Instrument (shown) or Ion
OneTouch™2 System)
3Ion Torrent™Server
4Local area network
5Internet
6Client computer
2
Ion Torrent S5™andIon Torrent S5™XL Instrument User Guide 9
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Torrent Browser
3
4
5
2
1
Figure 2 Ion Torrent S5™Sequencer configuration
1Ion Torrent S5™Sequencer
2Ion template preparation instrument (Ion
Chef™Instrument (shown) or Ion
OneTouch™2 System)
3Local area network
4Internet
5Client computer
Internet connectivity
The Ion Torrent S5™ Sequencer or the Ion Torrent™ Server should be connected to a
network with internet access. Connecting to the internet provides you the ability to
easily update your software and access remote system support. Software updates
through the network/internet are free. If you choose not to connect your instrument or
server to a network, software updates will need to be manually installed via USB.
IMPORTANT! The USB method for updating is not supported by Thermo Fisher
Scientific.
Any issues (file corruption, incomplete updates, etc.) updating the sequencer or server
in this manner requiring correction of the faulty update is not covered by your Ion
Torrent S5™ or Ion Torrent S5™ XL Sequencer warranty or any service contract you
may have purchased. You will be required to schedule an on-site Time and Materials
visit by a Thermo Fisher Scientific field service engineer to correct the problem at your
own expense.
In providing outbound access to the internet from the server, you enable the Thermo
Fisher Scientific support team to provide inbound support. Both the Ion Torrent S5™
Sequencer and the Ion Torrent™ Server run a remote monitor agent that can provide
service personnel with critical system information, such as installed software versions
and instrument alarms. With your permission, the agent also allows service personnel
to remotely log into the Ion Torrent S5™ Sequencer and the Ion Torrent™ Server, which
is required for system support. Without remote access, service personnel cannot
access, view, and troubleshoot issues regarding machine performance.
To enable full support, the Ion Torrent™ Server must have outbound internet access
(ports 22, 80, and 443) and be behind an appropriately configured firewall. While not
recommended, you can enable access to the Ion Torrent™ Browser (the web server
running on the Ion Torrent™ Server from the Internet). If you provide such access, you
must restrict access to the server using HTTP and AUTH firewall rules, or a
Chapter 2 System components
Internet connectivity
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combination of the two. Implementing and maintaining such restrictions is the
responsibility of the customer's server administrator and not of Thermo Fisher
Scientific.
Note: For answers to common questions about Ion Torrent™ Server network access
requirements, refer to the frequently asked questions (FAQ) and the Torrent Server
Administrator Guide in the Torrent Suite section of the Ion Community website (http://
ioncommunity.lifetechnologies.com). The FAQ provides information that you can
use to prepare Ion Torrent S5™ Systems and servers within the umbrella policies of
your site.
Ion Torrent S5™System component positions
7
1
2
3
5
6
4
1Touchscreen
2Reagent cartridge
3Power button
4Chip clamp
5Primary Wash solution bottle (W2
position). Waste reservoir located behind
the W2 bottle (shown on the right).
6Secondary Wash solution bottle (W3
position)
7Waste reservoir
Note: The system utilizes RFID technology to verify that the proper reagents are
loaded in positions 2, 5, and 6. Reagents that exceed their expiration date or usage
count will generate an error message prompting the user to replace the reagent before
performing the run.
Note: RFID regulatory information can be found on the main screen under Options
then Regulatory info.
Chapter 2 System components
Ion Torrent S5™System component positions
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Ion Torrent S5™and Ion Torrent S5™XL Sequencer input and output
connections
1
2
3
4
1USB ports – Connects the barcode reader
to the instrument.
2Ethernet port – An RJ45 port that provides
Ethernet (Gigabit) communication with the
Ion Torrent S5™or Ion Torrent S5™XL
Sequencer.
3On/off switch – Power switch, where the
states are on ( | ) or off ( O ).
4Power port – 100-240VAC port that
provides power to the instrument.
Chapter 2 System components
Ion Torrent S5™and Ion Torrent S5™XL Sequencer input and output connections
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Create a Planned Run
IMPORTANT! This sequencing kit is compatible with Ion Torrent™ System 4.4 and
later. Before proceeding, check for updates to the Ion Torrent™ System and Ion
Torrent S5™ or Ion Torrent S5™ XL Sequencer software, and install the updates if
available.
Note: If you are currently using Ion Reporter™ Software v1.4 with an earlier version
of the Torrent Suite™ Software, contact Technical Support for assistance with
upgrading to Ion Torrent™ System 4.4.
About planned runs
Planned runs contain all the settings used in a sequencing run, including number of
flows, kit types, barcodes used (if any), run type (e.g., DNA, RNA, amplicons), and
reference file (if any). They provide a fast and convenient way to set up and organize
your runs.
You create planned runs using the Torrent Browser and then select the appropriate
plan in the Select Planned Run screen of the Ion Torrent S5™ or Ion Torrent S5™ XL
Sequencer when you are ready to perform the run (see t_Start the sequencing run).
Note: For additional information, see the Torrent Suite™ User Interface Guide, available
on the Ion Community at ioncommunity.lifetechnologies.com.
Create a planned run
1. Open Torrent Browser for the Ion Torrent™ Server connected to your Ion Torrent
S5™ or Ion Torrent S5™ XL Sequencer .
2. Select the Plan tab, select Templates, locate the application you want to run (for
example, AmpliSeq DNA), then select:
•Upload Plans to upload a .csv format file containing your run information.
•Plan New Run to plan a new run using the generic template for the selected
application.
•Add New Template to create a new planned run template that you can
reuse for the selected application.
• Other options that may be available depending on your selected application,
such as downloading designs from AmpliSeq.com.
3. When you have completed your selections, click Plan Run to save your
selections. The run is listed on the Planned Runs page under the name you
specified.
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Planned run wizard: key fields
Field name Description
IonReporter If Ion Reporter™Software is installed and enabled and you want to
analyze the run data using the software, select the account and
workflow.
Application Select the sequencing application you are performing.
Library Kit Type Select the kit used to prepare the library.
Template Kit Select the instrument and kit used to prepare the templated Ion
PI™Ion Sphere™Particles.
Sequencing Kit Select the Ion Torrent S5™Sequencing Kit.
Chip Type Select the chip type you are using.
Flows Enter the appropriate number of flows for the sequencing kit and
read length.
Barcode Set
(optional) If you are using barcodes with:
•DNA libraries: Select the IonXpress barcode set, which
includes all barcodes in the Ion Xpress™Barcode Adapters
1‑96 Kits.
•RNA libraries prepared using the Ion Total RNA-Seq Kit v2:
Select the IonXpressRNA barcode set, which contains all 16
barcodes in the Ion Xpress™RNA BC01-16 Kit.
If you are not using barcodes with:
•DNA libraries: Leave the Barcode field blank.
•RNA libraries prepared using the Ion Total RNA-Seq Kit v2:
Select RNA_Barcode_None from the drop-down list. This will
ensure that the proper trimming is performed on the
resulting sequence when the RNA library does not have a
barcode.
Plugins Select and configure the appropriate plugins for your application.
Project Select or add a project within which to group your run data. You
can include runs in multiple projects, and remove runs from a
project at any time.
Run Plan Name Enter a name for the run.
Reference Library Select a reference library uploaded to the Torrent Server, if any.
Target Regions and
Hotspot Regions Select the Target Regions and/or HotSpot Regions BED file on the Torrent Server, if any.
Chapter 3 Create a Planned Run
Planned run wizard: key fields
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Field name Description
Enter a sample
name... Specify the Sample Name, ID, and Description for each sample in the run (number of samples will change based on the number of
barcodes and/or chips selected).
Monitoring
Thresholds Set thresholds for Bead Loading, Key Signal, and Usable Sequence. In the Ion Proton™Torrent Browser Monitor4Runs in
Progress tab, an alert is displayed if the values for a run fall below
the selected thresholds.
Chapter 3 Create a Planned Run
Planned run wizard: key fields
3
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Instrument operation
Power the Ion Torrent S5™or Ion Torrent S5™XL Sequencer on or
off
Note: If the Ion Torrent S5™ Sequencer is powered on, and the touchscreen is blank,
touch the screen to "wake" the touchscreen.
1. Locate the power switch on the back of the instrument and turn to the on (|)
position.
2. Press the power button on the left side of the instrument. The button should
illuminate. When the instrument touchscreen Main Menu appears, the
instrument is ready for use.
It is not necessary to power off the instrument overnight or over the weekend. If the
instrument will not be used for more than 3 days, power off the instrument as follows:
1. In the Main Menu, select Tools > Shut Down.
2. Ensure the post-run cleaning is complete, then press Shut Down.
3. After you exit the main touchscreen, press the Halt button, then OK when
prompted. The instrument will power down.
Chip handling guidelines
To place a loaded chip in the chip clamp:
Reviewer: need new photos for this process
Slide the metal tab out to access the chip
holder.
4
Power on
Power off
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If necessary, remove the chip currently in
the clamp.
Place the appropriate loaded chip in the
chip clamp with the chip notch in the
bottom ‑front corner.
Note: Do not force the chip into the clamp.
If the chip does not fit easily in the clamp,
confirm that the notch is oriented as shown
in the photo.
Slide the metal tab in until it clicks to
engage the clamp.
Close the instrument door. need new photo of closing the door.
Select the planned run and perform the run
Prepare and load the Ion 520™, Ion 530™, or Ion 540™ Chip before performing this
procedure.
1. Secure the chip loaded with template-positive Ion Sphere™ Particles in the chip
clamp, close the instrument door, then press Next.
2. In the drop-down list, select a planned run that you created in the Torrent Suite
Software, then press Next.
Note: You can also select Planned Run (none), then enter your run information
on the following screen, but selecting a predefined planned run is recommended.
3. Confirm the pre-populated settings are correct, or make changes using the
buttons and drop-down lists if necessary.
Chapter 4 Instrument operation
Select the planned run and perform the run
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4. Confirm that the instrument door is closed, then press Next to begin the
sequencing run.
The system calibrates the chip (~1 minute), then begins the sequencing run. If
chip calibration fails, see ts_Error message: Failed: Reseat chip then press Next to
recalibrate_Ion Proton Sequencer.
IMPORTANT! During a run, do not open the instrument door, and avoid
touching the instrument. Touching the instrument during the sequencing run
may reduce the quality of the measurements.
When the run is complete, the touchscreen returns to the Main Menu. Use the Torrent
Suite Browser to review the results.
Update the Ion Torrent S5™System software
Note: An internet connection is required for the Ion Torrent S5™ System to receive
alerts that software updates are available.
If an update to the Ion Torrent S5™ Sequencer software is available, the red “Alarms
and Events” pop-up appears in the touchscreen Main Menu to alert you. Press the red
pop-up to see the detailed messages. If a message states New Software Available,
update the software as follows:
Reviewer: How do users with instruments not connected to the internet receive
notification that software updates are available, and how do they update the
software?
1. In the Main Menu, select Options4Updates.
2. Select the Released Updates checkbox, then press Check.
3. When the message Press Update to begin update process appears, press Update.
Note: If the message All Software Current appears, press Back to return to the
Main Menu.
4. In the warning/confirmation dialog, press Ok. The software update progress bar
will appear.
5. When the message Update Done displays, follow the onscreen prompts to restart
the instrument.
IMPORTANT! After updates are installed, the instrument must be restarted.
Note: In some cases, the instrument restarts automatically after software
installation.
Chapter 4 Instrument operation
Update the Ion Torrent S5™System software
4
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Clean the instrument
Required materials:
• absorbent paper towels
• isopropyl alcohol (IPA) wipes
•(optional)– 10% bleach solution
To clean or decontaminate the instrument in the event of a spill or leak on or inside
the instrument:
Note: Dispose of all waste in appropriate liquid or solid waste containers.
1. Remove the W2 reagent bottle, then remove and empty the waste reservoir.
2. Remove the nucleotide reagent cartridge.
3. Visually inspect the waste and nucleotide reagent bays for liquid.
4. Using absorbent paper soak up as much liquid as possible, then wash the
affected area with 10% bleach solution.
5. Wipe the affected surfaces with IPA wipes, then allow to air-dry.
Chapter 4 Instrument operation
Clean the instrument
4
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Touchscreen reference
Clean, Initialize, and Run
The Clean, Initialize, and Run programs lead you through the necessary steps to
prepare the instrument for sequencing and start a sequencing run.
• The Clean program can be used to perform a wash solution cleaning. Cleaning
must be performed before each initialization to ensure that the reagents from the
previous run are cleared from the fluid lines. Follow the instructions provided on
the touchscreen.
• The Initialize program must be performed before each run to prepare the run
reagents. The Initialize program walks you through the following steps:
– Specifying the sequencing kit.
– Loading the reagent and wash solutions. (After this step, the instrument
performs a reagent check.
Abbreviated instructions are provided on the touchscreen; for detailed
instructions, see .
• The Run program walks you through steps leading up to and through
sequencing, including:
– Placing a loaded chip on the instrument.
– Selecting a planned run created in the Torrent Server Software.
– Performing sequencing.
A
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