0.3.0

• GTDB-Tk v0.3.0 has been released (we recommend all users update to this version):
  • Best translation table displayed in summary file.
  • GTDB-Tk now supports gzipped genomes as inputs (--extension .gz).
  • By default, GTDB-Tk uses precalculated RED values.
  • New option to recalculate RED value during classify step (--recalculate_red).
  • New option to export the untrimmed reference MSA files.
  • New option to skip_trimming during align step.
  • New option to use a custom taxonomy file when rooting a tree.
  • New FAQ page available.
  • New output structure.
  • This version requires a new version of the GTDB-Tk data package (gtdbtk_r89_data.tar.gz) available here

0.2.2

• Fix scratch_dir (--mmap-file) option.

0.2.1

• GTDB-Tk v0.2.1 has been released (we recommend all users update to this version):
  • Species classification is now based strictly on the ANI to reference genomes
  • The "classify" function now reports the closest reference genome in the summary file even if the ANI is <95%
  • The summary.tsv file has 4 new columns: aa_percent, red_values, fastani_reference_radius, and warnings
  • By default, the "align" function now performs the same MSA trimming used by the GTDB
  • New pplacer support for writing to a scratch file (--mmap-file option)
  • Random seed option for MSA trimming has been added to allow for reproducible results
  • Configuration of the data directory is now set using the environmental variable GTDBTK_DATA_PATH (see pip installation)
  • Perl dependencies has been removed
  • Python libraries biolib, mpld3 and jinja have been removed
  • This version requires a new version of the GTDB-Tk data package (gtdbtk.r86_v2_data.tar.gz) available here

0.1.6

• align step in classify_wf and de_novo_wf function has been fixed.
• improve summary file output.
• "align" function now supports the same custom trimming GTDB will be performing.
• returns closest reference genome to summary file (even if the ANI is less than 95%)
• bug fixing

0.1.3

• v0.1.3 resolves bug that would occur when a user genome has a FastANI >= 95% with reference genomes but not with the closest pplacer leaf node.

0.1.2

Release 0.1.2 addresses a bug that would occasionally cause genomes to not be correctly associated with a reference genome in the pplacer tree. FastANI was still identifying correct species assignments.

0.1.1

• config_template.py updated
• rooting of the tree is now fixed.

0.1.0

• GTDB-Tk is now using archived (.gz) fna files.
• Optimised for R86 version
• summary.tsv file is now the main output file.
• fastani.tsv file is now combined with summary.tsv.
• red_value.tsv file has been removed.
• Each Pplacer placement on a species branch is now verify by FastANI and the ANI is compared with all other species in the same genus to check Pplacer accuracy.
• New functionality: "trim_msa" allows to trim an untrimmed MSA (41155AA for bac120 and 32675AA for ar122) based on GTDB-Tk masks

0.0.6

• Migration to R83 and integration of UBA genomes
• add "debug" flag to classify options
• error handling improvement

0.0.5

Small bug fix