Jun 13, 2025

Public workspaceDownload Sequences from Eurofins - Edit Filenames for Use in Geneious

DOI
https://dx.doi.org/10.17504/protocols.io.eq2ly3bjegx9/v1
  • Dakota Betz1
  • 1ucsd
  • Rouse Lab
Marina McCowin
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DOI: https://dx.doi.org/10.17504/protocols.io.eq2ly3bjegx9/v1
Protocol Citation: Dakota Betz 2025. Download Sequences from Eurofins - Edit Filenames for Use in Geneious. protocols.io https://dx.doi.org/10.17504/protocols.io.eq2ly3bjegx9/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: June 13, 2020
Last Modified: June 13, 2025
Protocol Integer ID: 38171
Keywords: download sequences from eurofin, eurofin, download sequence, edit filenames for use, edit filename, geneious, document, old version, sequence, protocol
Disclaimer
Our protocols are constantly evolving and old versions will be deleted.
The documents here are not intended to be cited in publications
Abstract
Our protocols are constantly evolving and old versions will be deleted.
The documents here are not intended to be cited in publications
Guidelines
This protocol is optimized for Macs for use with the bash terminal.
Troubleshooting
Download sequences from Eurofins (you should have a link in your email). Once downloaded, unzip the folder.
Optional: Search your four letter code (use command F in Finder) in the Eurofins folder and move all of your sequence files to another folder that is easy to navigate to.

For example, create a new folder called Date_Seqs on your Desktop and paste all of the sequences you found with your four letter code there.
Open the bash terminal and navigate to the folder with your sequences in it (use the cd command and the path to the folder).

If you're following the example, see below. Note that all commands will be written in the text in bold, while items in italics indicate parts of the commands that are specific to you and therefore likely to change from the example (see above; includes file/folder paths, sample names, etc).
Command
new command name
cd Desktop/Date_Seqs



Once you've navigated to the folder with your sequences in it, paste in the following to replace your four-letter code with an underscore: for file in *code*; do mv "$file" "$file//code/_}; done
Be sure to replace "code" with the four-letter code that is specific to you/your files.
Command
new command name
for file in *code*; do mv "$file" "${file//code/_}"; done

Output: Check that all of your files have been renamed. In the above example, all instances of "code" have now been replaced with an underscore. You should see the same result. You can now proceed with bringing your .ab1 files into Geneious and assembling them as per usual.