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MAINT: use new_taxdump in fetch-ncbi-taxonomy? #124

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Sann5 opened this issue Jan 23, 2024 · 0 comments
Open

MAINT: use new_taxdump in fetch-ncbi-taxonomy? #124

Sann5 opened this issue Jan 23, 2024 · 0 comments
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enhancement New feature or request

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@Sann5
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Sann5 commented Jan 23, 2024

  • The fetch-ncbi-taxonomy action downloads the taxdump data from the NCBI Taxonomy FTP server so it can be used by the build-sutom-diamond-db action to create a Diamond database.
  • This taxdump data is the same that is used in the Diamond tutorial, however the NCBI Taxonomy FTP server also has what they called new_taxdump, what we believe is an updated version of the "old" taxdump data.
  • We would like to explore replacing the old taxdump data with the new, taking care that it is compatible with the downstream Diamond database creation.

Relevant documentation: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7408187/

@Sann5 Sann5 added the enhancement New feature or request label Jan 23, 2024
@Sann5 Sann5 self-assigned this Jan 23, 2024
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