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Make tree for 450bp of the N gene ("N450") #20

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Merged
kimandrews merged 11 commits into from
Apr 1, 2024
Merged

Make tree for 450bp of the N gene ("N450") #20

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55ea0ce
Add reference files for N450 region
kimandrews Mar 21, 2024
edbefd5
Prepare N450 sequences for phylogenetic analysis
kimandrews Mar 21, 2024
8343876
Construct phylogeny for N450 region
kimandrews Mar 21, 2024
d55342b
Annotate phylogeny for N450 region
kimandrews Mar 21, 2024
ab92a1b
Export phylogeny for N450 region
kimandrews Mar 21, 2024
f39ba8b
Use `--stochastic-resolve` option for `augur refine`
kimandrews Mar 28, 2024
119fbcf
Remove "country" colors from `defaults/colors.tsv`
kimandrews Mar 28, 2024
862dbaf
Change default display to rooted time-tree
kimandrews Mar 28, 2024
8bea320
Use `--metadata-columns` to export "author" in auspice_config.json
kimandrews Mar 28, 2024
a9d2644
Organize builds as directories within `results`
kimandrews Mar 28, 2024
bf83a42
Update Changelog
kimandrews Apr 1, 2024
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2 changes: 2 additions & 0 deletions phylogenetic/Snakefile
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Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
genes = ['N450', 'genome']

configfile: "defaults/config.yaml"

rule all:
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12 changes: 6 additions & 6 deletions phylogenetic/rules/construct_phylogeny.smk
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Expand Up @@ -7,9 +7,9 @@ See Augur's usage docs for these commands for more details.
rule tree:
"""Building tree"""
input:
alignment = "results/aligned.fasta"
alignment = "results/aligned_{gene}.fasta"
output:
tree = "results/tree_raw.nwk"
tree = "results/tree_raw_{gene}.nwk"
shell:
"""
augur tree \
Expand All @@ -26,12 +26,12 @@ rule refine:
- filter tips more than {params.clock_filter_iqd} IQDs from clock expectation
"""
input:
tree = "results/tree_raw.nwk",
alignment = "results/aligned.fasta",
tree = "results/tree_raw_{gene}.nwk",
alignment = "results/aligned_{gene}.fasta",
metadata = "data/metadata.tsv"
output:
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@jameshadfield jameshadfield Mar 25, 2024

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The temporal signal is much better in this build (and the build Trevor showed me) than the one we looked at mid-week - do you know what changed? This gives me more confidence that the (temporal) rooting is working ok for the N450 build - it's broadly similar to the genome build - and so there's no longer a need to start in "unrooted" view if you'd prefer to go back to the more typical rectangular view.

image

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@kimandrews kimandrews Mar 25, 2024

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The lower temporal signal for the tree I showed you last week seems to be related to the subsampling method I had used. Here is the subsampling method I used for that tree:

filter_N450:
group_by: "country year month"
sequences_per_group: 2
min_date: 1950
min_length: 400

And here is the clock view for a tree I generated today using that subsampling method:

image

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@kimandrews kimandrews Mar 28, 2024

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Changed default display back to rooted time-tree in 862dbaf

tree = "results/tree.nwk",
node_data = "results/branch_lengths.json"
tree = "results/tree_{gene}.nwk",
node_data = "results/branch_lengths_{gene}.json"
params:
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@jameshadfield jameshadfield Mar 25, 2024

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The following deprecation notice is present when running refine:

        DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving
        polytomies using the old 'greedy' mode. This is not well suited for large
        polytomies. Stochastic resolution will become the default in future
        versions. To switch now, rerun with the flag `--stochastic-resolve`. To
        keep using the greedy method in the future, run with `--greedy-resolve`

Especially for the N450 build where we will have large polytomies we should use --stochastic-resolve.

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@kimandrews kimandrews Mar 28, 2024

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Done in f39ba8b

coalescent = config["refine"]["coalescent"],
date_inference = config["refine"]["date_inference"],
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