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Commits on Oct 11, 2024

• Merge pull request #2 from Ecogenomics/remove_mash

  Show description for d24a49e
  donovan-h-parks

  authored
  d24a49e

• feat: removed mash prefiltering in favour of just using skani; set skani to run in default mode with -s = 85

  donovan-h-parks

  committed
  9752a85

Commits on Apr 10, 2024

• feat: better tracking of name assignments and additional rule to ensure use of previous placeholder names where appropriate

  donovan-h-parks

  committed
  1f06c29

• fix: proper assignment of alphanumeric specific name when GTDB genus is alphanumeric

  donovan-h-parks

  committed
  1d70492

• feat: updated for R220 species clusters

  donovan-h-parks

  committed
  cb7a9e8

Commits on Oct 16, 2023

• fix: small fixes required for R220 due to changing file formats or issues with move from FastANI to skani

  donovan-h-parks

  committed
  6db8ee6

Commits on Oct 3, 2023

• feat: minor logging update

  donovan-h-parks

  committed
  740d55f

Commits on Sep 28, 2023

• feat: fix to how genomes are assigned to the final set of representative genomes; improve documentation regarding edge case where a genome is not in the ANI radius of its closest representative

  donovan-h-parks

  committed
  26472f0

Commits on Sep 11, 2023

• feat: finish migration from FastANI to skani; fixed bug in creation of de novo species clusters

  donovan-h-parks

  committed
  53bee90

Commits on Jul 25, 2023

• feat: move from FastANI to skani

  donovan-h-parks

  committed
  01ccaa5

Commits on May 21, 2023

• Updates for R214

  donovan-h-parks

  committed
  2110fee

Commits on Jan 12, 2023

• Updates to reflect changes in GTDB-Lib

  donovan-h-parks

  committed
  ae32059

• Update to reflect NCBI using not used as type instead of untrustworhty as type

  donovan-h-parks

  committed
  9c197d1

Commits on Jan 11, 2023

• Factored out all references to BioLib and moved any required functionality to GTDB-Lib.

  donovan-h-parks

  committed
  ed29816

Commits on Jan 10, 2023

• Added config.py.

  donovan-h-parks

  committed
  d96ad4b

• Improved documentation and added type hinting to update_resolve_types.py.

  donovan-h-parks

  committed
  780946e

• Updated all files to use the new rich logger.

  donovan-h-parks

  committed
  dda552d

Commits on Jan 9, 2023

• Improved documentation and added type hinting to update_lpsn_ssu_types.py

  donovan-h-parks

  committed
  6e4c3be

Commits on Jan 7, 2023

• Improved documentation of update_gtdbtk.py, added type hinting, and moved code to GTDB-Lib.

  donovan-h-parks

  committed
  1a468c3

Commits on Jan 6, 2023

• Improved update_qc_genomes.py documentation, added type hinting, and did minor code refactoring.

  donovan-h-parks

  committed
  5038fe1

Commits on Jan 5, 2023

• Updated logging to use GTDB-Lib; updated update_new_genomes.py to use GTDB-Lib and type hinting, and improved documentation

  donovan-h-parks

  committed
  465080c

• Codebase used to establish R214 species clusters.

  donovan-h-parks

  committed
  cece754

Commits on Jun 29, 2022

• Updated genome QC to use 2000 instead of 1000 contigs and to use the ar53 instead of the ar122 marker set

  donovan-h-parks

  committed
  872fba7

• Minor interface updates

  donovan-h-parks

  committed
  e8ddf2d

Commits on Mar 19, 2022

• GTDB R207 species clustering and naming

  donovan-h-parks

  committed
  834f2fc

Commits on Dec 3, 2021

• modified u_curation_trees so all genomes in a GTDB species cluster are considered and not just the representative genome

  donovan-h-parks

  committed
  bcc0487

Commits on Nov 8, 2021

• Added validation test for alphanumeric generic names with suffixed Latin specific names.

  donovan-h-parks

  committed
  eed48f6

Commits on Oct 22, 2021

• Updated GTDB-Tk script to user multiple CPUs with pplacer

  donovan-h-parks

  committed
  57019bf

Commits on Oct 21, 2021

• Changed marker set criterion back to 40%; determined that changing this to 50% impacted 443 species reps

  donovan-h-parks

  committed
  9f99d8c

Commits on Oct 18, 2021

• Added validation tests for capitalization changes between parent/child taxa; add test to try and identify Latin-looking names that are in fact placeholder names

  donovan-h-parks

  committed
  e8adebe

Commits on Oct 6, 2021

• modified u_pmc_species_names to produce gtdb_sp_clusters.ncbi_sp.tsv file indicating NCBI species name of all genomes in a GTDB species cluster

  donovan-h-parks

  committed
  94a4d05

Commits on Sep 27, 2021

• Force species names in gtdb_type_strains.tsv ledger to be in the GTDB taxonomy string

  donovan-h-parks

  committed
  8230185

Commits on Sep 20, 2021

• Fix to handle rare case when trying to resolve mapping between current and previous representatives

  donovan-h-parks

  committed
  9172e87

• Genomes in ncbi_untrustworthy_sp_assignments ledger now no longer considered type strain genomes; better logging

  donovan-h-parks

  committed
  bcce850

Commits on Sep 16, 2021

• Default value of ANI_SYNONYMS was incorrectly set to 0.97 instread of 97

  donovan-h-parks

  committed
  59e67ec

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