Emerging lineages

General
1

Hi everyone. I need of a help. How do I add emerging lineages in the nextstrain? Would it just edit the emerging lineages (emerging_lineages.tsv) file and Clades (clades.tsv) and add new ones?

2

Hi @mattoslmp – those files are independent of each other, and specify the mutations which define the colourings and branch labels for “Emerging Lineages” and “Clade”, respectively.

You can edit the files themselves, or create your own separate TSVs and set them via

# your profile's builds.yaml file
files:
  emerging_lineages: <filename>
  clades: <filename>
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3

Thank you @james for your listening and detailed explanation. Do you know where can I get the nucleotide mutations that define the clade/lineages? I just found it in AAs on outbreak.info. Best.

4

We are using the following mutations for nextstrain: emerging lineages TSV and clades TSV. For specific naming systems you’ll have to check their documentation, and note that their approach may not always map cleanly onto the approach we use.

5

Dear @james , I would like include some lineages that aren’t in this list.

6

If you add your desired lineages to the relevant TSV file, along with the mutations which define them, then they will be included in the produced dataset :smiley:

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7

@mattoslmp: I add lineages / clades to these files by mousing over branches in the tree to find mutations associated with a specific clade of interest. We used mainly nucleotide mutations in these files, but you can define clades by amino acid mutations as well. This would look something like:

clade    gene  site  alt
example  S     501   Y

The clade will be called for the first node in the tree that has all the mutations specified in the file. For example, we call emerging lineage B.1.619 as:

B.1.619	nuc	5008	T
B.1.619	nuc	14403	T
B.1.619	S	936	    N
B.1.619	S	939	    F

where this identifies the first node in the tree with T at nucleotide site 5008, T at nucleotide site 14403, N at spike site 936 and F at spike site 939.

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