Geneious wrapper plugin for Nextclade

Geneious wrapper plugin to run Nextclade for clade assignment, mutations calling and quality checks of SARS-CoV-2 genomes. The plugin accesses Nextclade’s latest data set used to assign clades to SARS-CoV-2 sequencing data.

• Input: SARS-CoV-2 genome sequence(s). To run on multiple sequences, first create a sequence list in Geneious.
• Output: .txt report which is imported into Geneious

System requirements

• Geneious 2021.1.1 or later (for older versions it may be possible to install the plugin from source)
• Python 3
• Nextclade (Installation instructions)

Mac or linux

1. Download nextclade_linux_mac_x.x.gplugin
2. In Geneious, go to 'Tools' --> 'Plugins' --> 'Install plugin from a gplugin file' and select the gplugin file and click 'Install'. The plugin should now appear under the 'Tools' menu.
3. When running the plugin the user will be prompted to enter the path to the folder where Nextclade is installed on the computer and the path to the folder where Nextclade’s output files should be located.

Windows

1. Download nextclade_windows_x.x.gplugin
2. In Geneious, go to 'Tools' --> 'Plugins' --> 'Install plugin from a gplugin file' and select the gplugin file and click 'Install'. The plugin should now appear under the 'Tools' menu.
3. When running the plugin the user will be prompted to enter the path to the folder where Nextclade is installed on the computer and the path to the folder where Nextclade’s output files should be located.

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Installation from source

First install the Geneious Wrapper Plugin Creator.

Create wrapper plugin in Geneious

1. Go to 'File' --> 'Create/Edit Wrapper Plugin..'. Press '+New'
2. Step 1:
   • Fill in 'Plugin Name:' and 'Menu/Button Text:' of your choice.
   • 'Plugin Type:' select 'General Operation'.
   • 'Bundled Program Files (optional)'
   • Linux/mac: add the nextclade_linux_mac.py script under 'Linux' or 'Mac OSX' respectively.
   • Windows: add the nextclade_win.bat script under 'Windows' and the nextclade_win.py script under 'Additional Bundled Files'.
3. Step 2:
   • 'Sequence Type:' select 'Nucleotide only'.
   • 'Document Type:' select 'Unanaligned Sequences (1+)'.
   • 'Command Line'
     • Windows: '[inputFileNames] nextclade [otherOptions]'
     • Linux/Mac: '[inputFileNames] nextclade [otherOptions]’
   • 'Output'
     • Windows: 'File Name:' fill in 'nextclade_final.tsv' and select 'Format:' 'Text file (plain)'
     • Linux/Mac'File Name:' fill in 'nextclade_final.csv' and select 'Format:' 'Text file (plain)'
4. Step 3: Press 'Add' to add two user options (in this order):
   • 'Command Line Switch': pathToNextclade, 'Option Label': Nextclade path
   • 'Command Line Switch': pathToOutput, 'Option Label': Path for output files
     Both 'Command Line Switch' and 'Option Label' should be filled in, but can be modified.