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For Agilent NGS Workstation Option B
This README describes how to set up NGI Stockholms Nextera XT method for the Agilent NGS Workstation. This protocol can be used to prepare up to 96 samples with Illumina's Nextera XT kit.
- Agilent NGS Workstation
⚠️ Option B only - Consumables
- Eppendorf twin.tec 96 PCR plate (Eppendorf, cat# 0030 128.672 (int); 951020460 (US))
- Nunc deepwell 1.3 mL plate (Thermo Scientific, cat# 260251)
- ABgene 2.2 mL storage plate Mk.II (Thermo Scientific, cat# AB-0933)
- Deepwell plate adaptor on position 6 (Agilent Technologies, cat# G5498B#012) and supporting device file
- Labware definitions*
- Liquid classes definition*
* provided in all_labware_liquids.vzp
nextera.pro
all_labware_liquids.vzp
nextera_pcr.pro
nextera_spri.pro
nextera_xt_form.VWForm
nextera_xt_intermission1.pro
nextera_xt_runset.rst
nextera_xt_script.js
resources/1313497192_media_controls_light_pause.png
resources/1313497517_media_controls_light_play.png
resources/clear_inventory.bat
resources/clear_inventory.sql
Clone into https://github.com/ngi-automation/nextera-xt.git from the Protocol Files directory:
cd "C:\VWorks Workspace\Protocol Files"
git clone https://github.com/ngi-automation/nextera-xt.gitAlternatively, download the compressed folder from:
https://github.com/ngi-automation/nextera-xt/archive/master.zip
and extract to C:\VWorks Workspace\Protocol Files. Rename the resulting nextera-xt-master folder to nextera-xt. The path to the folder containing the extracted files should then be C:\VWorks Workspace\Protocol Files\nextera-xt.
Use the import feature in VWorks from File › Importin the toolbar and select the all_labware_liquids.vzp file included. See the VWorks Knowledge Base for more information.
Device files and profiles are system specific and will not be provided. The "standard" Bravo configuration is used in the Nextera XT protocols:
| Position | Type | Part# |
|---|---|---|
| 1–3, 8 | Deck Platepad | G5498b#004 |
| 4, 6 | Peltier Thermal Station (Inheco) | G5498b#021 |
| 5 | Orbital Shaking Station | G5498b#033 |
| 7 | Magnetic Bead Accessory | G5498b#008 |
| 9 | Thermal Station (ThermoCube) | G5498b#036/7/8 |
For reference see Agilent's accessories catalog for the Bravo.
.pro file must have the correct device file set.
See the VWorks Knowledge Base for more information on how to select the device file.
Instructions extracted from the NGI Stockholm/SciLifeLab SOP are available as a PDF file.
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
The full license can also be found in the file LICENSE and must included when redistributing the software.
If this method is used to generate results for publication we ask that you include a reference to this repository, something like:
Automation protocols made available by NGI Sweden at https://github.com/ngi-automation/nextera-xt
VWorks Automation Control, Bravo and other things relating to the Agilent NGS Workstation are trademarks owned by Agilent Technologies, Inc. (Santa Clara, CA 95052-8058, US).
Nextera XT is a trademark owned by Illumina, Inc. (San Diego, CA 92122 US)
National Genomics Infrastructure at SciLifeLab
joel.gruselius@scilifelab.se
July 2014 =======
An automated method for the Nextera Rapid Capture kit on the Agilent NGS Workstation (Option B)
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