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Published 20 hours ago • verified publisher icon nf-core

Mention AMPcombi and DRAMP database in usage.md

Open jasmezz opened this issue 1 year ago • 2 comments

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 avatar Apr 04 '24 09:04 jasmezz

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.

Darcy220606 avatar Apr 05 '24 09:04 Darcy220606

  • 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.

jasmezz avatar Apr 05 '24 12:04 jasmezz