ngi-automation/rad-seq

RAD-seq protocols for the Agilent NGS workstation option B.

Automated RAD-seq Installation Guide

For Agilent NGS Workstation Option B

Contents

1. Description
2. Requirements
3. Installation
4. Protocol
5. License

Description

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.

Requirements

Item	Note
Agilent NGS Workstation	⚠️ Option B configuration only
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

Included files

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

Installation

Download files

Using Git

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.git

Alternatively, 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.

Configure

Labware and and liquid class definitions

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

Device files and profiles are system specific and will not be provided. The "standard" Bravo configuration is used in the RAD-seq protocols:

Standard configuration

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.

⚠️ Each .pro file must have the correct device file set.

See the VWorks Knowledge Base for more information on how to select the device file.

Protocol

Instructions are available as a PDF file.

License

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).

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National Genomics Infrastructure at SciLifeLab
[email protected]
Nov 2017