For Agilent NGS Workstation Option B
This README describes how to set up NGI Stockholms RAD-seq method for the Agilent NGS Workstation. This protocol can be used to prepare up to 96 samples with the in-house RAD-seq protocol.
| Item | Note |
|---|---|
| Agilent NGS Workstation | |
| 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 |
| Labware definitions | Provided in all_labware_liquids.vzp |
| Liquid classes definition | Provided in all_labware_liquids.vzp |
README.md
all_labware_liquids.vzp
illumina_double-spri.pro
illumina_spri.pro
rad-seq.VWForm
rad-seq.js
rad-seq.rst
rad-seq_ligation.pro
rad-seq_pcr.pro
rad-seq_reaction.pro
rad-seq_setup1.pro
rad-seq_setup2.pro
rad-seq_setup3.pro
rad-seq_setup4.pro
rad-seq_setup5.pro
resources
resources/clear_inventory.bat
resources/1313497517_media_controls_light_play.png
resources/clear_inventory.sql
resources/1313497192_media_controls_light_pause.png
Clone into https://github.com/ngi-automation/rad-seq.git from the Protocol Files directory:
cd "C:\VWorks Workspace\Protocol Files"
git clone https://github.com/ngi-automation/rad-seq.gitAlternatively, download the compressed folder from:
https://github.com/ngi-automation/rad-seq/archive/master.zip
and extract to C:\VWorks Workspace\Protocol Files. Rename the resulting rad-seq-master folder to rad-seq. The path to the folder containing the extracted files should then be C:\VWorks Workspace\Protocol Files\rad-seq.
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 RAD-seq 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 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 the National Genomics Infrastructure Stockholm at https://github.com/ngi-automation/rad-seq
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).
National Genomics Infrastructure at SciLifeLab
joel.gruselius@scilifelab.se
Nov 2017