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Add template for phylogenetic description.md #48

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joverlee521 opened this issue Jun 28, 2024 · 1 comment
Open

Add template for phylogenetic description.md #48

joverlee521 opened this issue Jun 28, 2024 · 1 comment
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enhancement New feature or request

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@joverlee521
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Context

Originally brought up by @trvrb and @genehack on Slack.

Description

Since the pathogen ingest workflow has been pretty standardized around using public NCBI data, it makes sense to include a generic description.md to be used by phylogenetic workflows to acknowledge the source of the underlying data.

Examples

Possible solution

Recommended text:

We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequences and metadata for sharing their work. Please note that although data generators have generously shared data in an open fashion, that does not mean there should be free license to publish on this data. Data generators should be cited where possible and collaborations should be sought in some circumstances. Please try to avoid scooping someone else's work. Reach out if uncertain.

We curate sequence data and metadata from NCBI as starting point for our analyses. Curated sequences and metadata are available as flat files at:
data.nextstrain.org/files/workflows/{pathogen}/sequences.fasta.zst
data.nextstrain.org/files/workflows/{pathogen}/metadata.tsv.zst

@joverlee521 joverlee521 added the enhancement New feature or request label Jun 28, 2024
@joverlee521
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As noted in nextstrain/seasonal-cov#24 (comment), the listed data section should only be added if the files exist on S3 and the filepaths can differ based on whether the pathogen includes subtypes/segments that are in separate files.

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