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Mention AMPcombi and DRAMP database in usage.md #354

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jasmezz opened this issue Apr 4, 2024 · 2 comments
Open

Mention AMPcombi and DRAMP database in usage.md #354

jasmezz opened this issue Apr 4, 2024 · 2 comments
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documentation Improvements or additions to documentation enhancement Improvement for existing functionality

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@jasmezz
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jasmezz commented Apr 4, 2024

Description of feature

On the current dev branch, AMPcombi and how to provide its DRAMP database with --amp_ampcombi_db, is not mentioned in the usage.md (as is for all other database-using tools). Users should know that they can supply the database offline (although its only a few MB).

@jasmezz jasmezz added documentation Improvements or additions to documentation enhancement Improvement for existing functionality labels Apr 4, 2024
@Darcy220606
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I would also suggest that for the taxonomc classification we recommend the usage of GTDB due to its vast and curated taxonomic database. But for that the user needs more RAM and storage resources.

@jasmezz
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jasmezz commented Apr 5, 2024

  • And mention GTDB is huge. SILVA is an appropriate smaller alternative (better than default "Kalamari") for 16S-based classification, but might be not that stable in download.
  • SILVA ist included in GTDB.
  • Users should know which one they want.

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