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2.0.0

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@aaronmussig aaronmussig released this 08 Apr 01:54
· 292 commits to master since this release
2.0.0
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Major changes:

  • GTDB-TK now uses a divide-and-conquer approach where the bacterial reference tree is split into multiple order-level subtrees. This reduces the memory requirements of GTDB-Tk from 320 GB of RAM when using the full GTDB R07-RS207 reference tree to approximately 35 GB. A manuscript describing this approach is in preparation. If you wish to continue using the full GTDB reference tree use the --full-tree flag.
  • Archaeal classification now uses a refined set of 53 archaeal-specific marker genes based on the recent publication by Dombrowski et al., 2020. This set of archaeal marker genes is now used by GTDB for curating the archaeal taxonomy.
  • By default, all directories containing intermediate results are now removed by default at the end of the classify_wf and de_novo_wf pipelines. If you wish to retain these intermediates files use the --keep-intermediates flag.
  • All MSA files produced by the align step are now compressed with gzip.
  • The classification summary and failed genomes files are now the only files linked in the root directory of classify_wf.

Features:

  • convert_to_itol to convert trees into iTOL format (#373)
  • Output FASTA files are compressed by default (#369)
  • Intermediate files will be removed by default when using classify/de-novo workflows unless specified by --keep_intermediates (#369)
  • Add --genes flag for Error (#362)
  • A warning will be displayed if pplacer fails to place a genome (#360 / #356)

Important

  • This version is not backwards compatible with GTDB release 202.
  • This version requires a new reference package
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