A quick guide to importing primer sets from TSV/CSV files

Primer sets, such as those provided by the Artic network for tiled amplicon sequencing of SARS-Cov-2, can easily be imported into Geneious from tab or comma-delimited files. 

First, make a new folder in your database where you want the primers to go.  We recommend using a separate folder for each set of primers.  Then drag and drop the file containing your primers onto the Geneious window, and choose the format (TSV or CSV) at the prompt.  

importcsv.png

In the next window, ensure each column in the file is assigned to the correct field in Geneious, i.e the column containing the primer name is assigned to the Name field, and the sequence is in the Sequence field etc.  Choose Primer as the import type, and select "Determine Characteristics" to ensure that Tm values are added to the sequence.  

Importcsv2.png

Then click OK to import the sequences. 

 

Downloading primer sets from the Artic network

The Github repository of primer schemes is available at https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019.

Select the folder for the version you are using (e.g. V1, V2 or V3), within that folder is a .tsv file.   

V3_download.png

Select this file to open it, then click the "Raw" option highlighted in the screenshot below to display the file in plain text format.  

Screen_Shot_2021-09-15_at_11.56.55_AM.png

Then use control/command-A to select the contents of this file, and control/command-C to copy it.  

Screen_Shot_2021-09-15_at_9.49.49_AM.png

You can then paste it directly in Geneious as a .tsv file by right-clicking in the Geneious document table and choosing "Paste" from the menu.  The import will then proceed as described above and you will need to configure the columns and the import type as shown in the "Import Documents" screenshot above.  

 

 

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Comments

  • Avatar
    katie vigil

    Hi can you give more information how to download the primers off GitHub. I cant figure out how to download the sequences. Thanks!

  • Avatar
    katie vigil

    com.biomatters.geneious.publicapi.plugin.DocumentImportException at com.biomatters.iseek.plugin.fileimport.E.a(Importage.java:279) at com.biomatters.iseek.plugin.fileimport.FileImporterManager.a(FileImporterManager.java:683) at com.biomatters.iseek.plugin.fileimport.FileImporterManager.a(FileImporterManager.java:650) at com.biomatters.iseek.plugin.fileimport.FileImporterManager.a(FileImporterManager.java:535) at com.biomatters.iseek.plugin.fileimport.FileImporterManager.a(FileImporterManager.java:388) at com.biomatters.iseek.plugin.fileimport.v.run(FileImporterManager.java:309) at java.base/java.lang.Thread.run(Thread.java:829)

  • Avatar
    katie vigil

    This is my error.

  • Avatar
    Hilary Miller

    Hi Katie
    When you select the file of primers from Github, you'll need to then choose the "Raw" option to get a plain tab-delimited text format that you can copy and paste (unfortunately I can't upload images in the comments, but I'll amend the post above to show this).

    You can actually copy and paste the raw text directly into Geneious without an intermediate file. Just right click somewhere in the Geneious document table and go "Paste" and you'll then get a prompt for the format (choose tsv) and a window where you can specify which column is the sequence etc. The screenshots above show how to format the TSV import window so that they are imported as primers.

    Edited by Hilary Miller