Cyberduck User Guide

Downloading Illumina HiSeq/MiSeq data with Cyberduck

UAGC and BCF support transmission of NGS data using Cyberduck file transfer system. Using a wired (NOT wireless) connection to the internet, follow the steps below.  Follow the steps below to get started. 

Download and Install Cyberduck-

1. Visit  and select the download compatible with your operating system. 

2. Open the Cyberduck.exe file and click "Install"


PC-users: It is not necessary to click this checkbox in the Installation Options. 


Download and Install the UAGC Cyber Duck Profile

1. Click here to download the UAGC Cyberduck Profile. Right click this link and select "Save Link As" and save on your computer.

(Note: If you can not save this file directly, open the XML text and copy all of the text below the horizontal line - starting  with <plist and  ending with plist>. Paste text into a text document and save this file as UAGC.cyberduckprofile)

2. Double click on this Profile where it is saved on your computer to launch Cyberduck. When you double click on the profile it will launch Cyberduck and auto populate relevant access data.   

3. Enter the UAGC/BCF username provided to you in the email regarding your dataset. 

4. Now you will be able to download your data and save to the location of your choosing. 


If you are having trouble with iRODs login through Cyberduck, try clicking on the “Open Connection” button at the top left, select ‘University of Arizona Genetics Core Data Download’ from the dropdown at the top of the window that pops up, then enter your username/password.