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.
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.
Then click OK to import the sequences.
Primer sources for Sars-Cov-2 analysis
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.
Select this file to open it, and copy the contents into a basic text editor (do not use Word). Save the file with a .tsv suffix, then drag and drop it into Geneious to import it as described above.
CDC Multiplex and Singleplex PCR primers
The Github repository of Sars-Cov-2 sequencing protocols is available at https://github.com/CDCgov/SARS-CoV-2_Sequencing/tree/master/protocols/CDC-Comprehensive
Select either the Multiplex_PCR or Singleplex_PCR folder, within that folder is a .tsv file containing the primers.
Select this file to open it, and copy the contents into a basic text editor (do not use Word). Save the file with a .tsv suffix, then drag and drop it into Geneious to import it as described above.
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