Fix: update dropped strains file to list accession instead of strain names #26
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victorlin
approved these changes
Feb 12, 2024
Rename the file dropped_strains.txt to exclude.txt to better reflect its purpose since it lists accession numbers instead of strain names. This file is a list of sequences to exclude from analysis and gets passed to `augur filter --exclude`.
joverlee521
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to nextstrain/pathogen-repo-guide
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Feb 13, 2024
Based on conversation in dengue PR nextstrain/dengue#26 (comment)
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Description of proposed changes
In the phylogenetic workflow, we initially listed strains slated to be dropped from the build (due to excessive divergence or misclassification) in the config/dropped_strain.txt file, identified by their strain names. Subsequently, we transitioned to using "accession" numbers to identify strains after merging the ingest pipeline (and using ncbi-datasets api) 8ab810f. However, updating the corresponding dropped strain list was missed resulting in these strains not being appropriately dropped from the build.
This commit addresses this issue by adding accession numbers to ensure proper dropping of these records.
Steps to find accessions:
metadata.tsvfile, the associated accession numbers are used.(e.g.
DAK_Ar_510is probably a shorter name forDENV2/COTE_D_IVOIRE/DAKAR510/1980)metadata.tsvfile for those collected in the same year and country, considering potential differences in underscores or hyphens separating the strain name (e.g.DENV1/VIETNAM/BIDV992/2006equivalent toDENV-1/VN/BID-V992/2006).DENV/SPAIN/EEB17/2009led to https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3149010/ which led to accession numberJF260983)Related issue(s)
Checklist
Post Merge rebase and update checklist