Add nextclade workflow [#2]
#10
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genehack
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It's intentional — the strains in the |
genehack
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Built from [nextclade workflow in yellow fever repo](nextstrain/yellow-fever#10)
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| Filtering to defined set of strains with known genotypes. |
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Haven't completely finished reviewing, but wanted to flag the reference tree only included 122 genomes when I ran this workflow locally. Not sure if that's intentional, but that seems low to me.
It's intentional — the strains in the
includefile are extracted from the 2 papers that defined the genotypes that are being assigned. The point of this dataset is to bootstrap a genotype-defining tree. The NCBI dataset (which is ~2000 sequences) doesn't have any systematic genotype annotation (at least, that I've been able to find), so these 122 are the only sequences with definitive genotypes.
Ah gotcha, that's good to know. Looking at the reference tree docs:
The tree should be sufficiently large and diverse to meet clade assignment expectations of a particular use-case, study or experiment.
It's not clear to me if 122 sequences is enough for a reference tree in Nextclade, but maybe we start here and handpick other sequences to include later 🤷♀️
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It's not clear to me if 122 sequences is enough for a reference tree in Nextclade, but maybe we start here and handpick other sequences to include later 🤷♀️
nod I know I don't know enough to have an opinion here. I opened a PR to add this to nextclade_data, so perhaps this conversation will happen in that context.
Addressed all your other comments; will plan on merging this early next week sans other feedback.
nextclade/defaults/colors.tsv
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Just wanted to flag that the group usually has an aversion to neon colors 🙈
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Is there a set of "acceptable" colors? When I was using the default ones, because of how they were assigned, it was super hard to distinguish between (e.g.) West Africa I and West Africa II, because they were both shades of dark blue.
I picked these semi-randomly by just shuffling around hex values, but I like that they're all clearly distinguishable to me.
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Is there a set of "acceptable" colors?
I usually just pick colors from Auspice
.markdownlintrc
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OH, markdownlintrc is new to me. Is this going be used in pre-commit?
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I haven't hooked it up there yet, but it could be!
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Built from [nextclade workflow in yellow fever repo](nextstrain/yellow-fever#10)
Built from [nextclade workflow in yellow fever repo](nextstrain/yellow-fever#10)
Description of proposed changes
This adds a workflow to build a Nextclade tree based on a set of genotype references extracted from two papers.
Related issue(s)
#2
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