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Using Nextclade web application

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Marit Hetland edited this page Feb 13, 2021 · 2 revisions

Nextclade is run in the pipeline to assign lineage and list mutations in the consensus sequences. To investigate the relationship between samples further, you can use the nextclade web application: https://clades.nextstrain.org/

  1. Save the consensus.fasta files of the sequences you are interested in visualising in a tree to one file, for example if you want to take all of the consensus.fasta files from your run, do: cat *consensus.fasta >> sequences.fasta

  2. Then head over to https://clades.nextstrain.org/ where you click "Select a file" and choose the sequences.fasta file. This will take a few moments to load, and you should be able to see some QC information and mutation information for your samples.

  3. Click "Show Tree"

  4. This will show you a phylogeny which includes reference strains (grey dots) from different lineages and the sequences that you uploaded from sequences.fasta (red dots). You can hover the mouse over any sample to see their name and mutations. You can also see the CLADE names on the branches. You can switch from viewing CLADE names to viewing aaSubstitutions.

  5. To zoom in on a clade, click on the branch of the clade you want to zoom in on. If you have samples where you suspect an outbreak and they all have the same clade, this can be useful to see if all of the samples cluster together or if they fall differently in the phylogeny with the reference clade sequences.

  6. Highlight a clade. You can filer/highlight clades too. Click "Filter tree" and in the box "by Clade" select the clade(s) you want to zoom in on. Click "Filter Tree" again to remove the filter box. The clade you chose should now be highlighter (darker lines than the rest).

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