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2.7.0

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@aaronmussig aaronmussig released this 15 Apr 05:03
· 38 commits to master since this release
2.7.0
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Release 2.7.0+ updates GTDB-Tk to use the latest GTDB R232 taxonomy and requires a new reference package. It includes the following new features:

  • Pre-sketched skani database: GTDB-Tk now uses a skani pre-sketched database of the GTDB representative genomes. This significantly reduces the database storage footprint from 198 GB (in Release 232) down to 98 GB.
  • Representative genomes availability: The GTDB representative genomes are now available via the "Download" page on the GTDB website.
  • Deprecated flag: Because the database is already sketched natively, the --skani_sketch_dir flag is now deprecated.
  • Replaced --skip_ani_screen with --place_species: The --skip_ani_screen flag is now deprecated in v2.7.0 and has been replaced by the --place_species flag. The logic has been updated to reflect the new database structure:
    • Previously: Using --skip_ani_screen, genomes placed in a genus by pplacer were only compared to representative genomes within that specific genus.
    • Now: Because the database is a single skani sketch, user genomes are compared against all GTDB reference genomes once at the very beginning of the pipeline. When the new --place_species flag is selected, the genomes are still explicitly placed in the reference tree.

⚠️ IMPORTANT MEMORY WARNING: The divide-and-conquer approach now requires more than 128 GB of RAM. Specifically, you will need at least 140 GB of RAM for R232.

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