Issues

• NCBI "scientific name" does not include all reasonable specific epithets, causing missed LPSN connections

  Ecogenomics/GTDBNCBI#58 · Filter by author Artoria2e5 opened on Jan 23, 2026
  3

• Field indicating isolate or environmental genome.

  enhancement
  Ecogenomics/GTDBNCBI#51 · Filter by author donovan-h-parks opened on Oct 22, 2018

• Export representatives

  Ecogenomics/GTDBNCBI#46 · Filter by author donovan-h-parks opened on Sep 1, 2017

• Check revised annotation for all type strains

  Ecogenomics/GTDBNCBI#44 · Filter by author donovan-h-parks opened on Jun 24, 2016

• Trimming columns with insufficient taxa is slow

  Ecogenomics/GTDBNCBI#36 · Filter by author donovan-h-parks opened on Apr 5, 2016

• Update User genome taxonomy

  Ecogenomics/GTDBNCBI#35 · Filter by author donovan-h-parks opened on Mar 23, 2016

• Calculating and storing metadata is time consuming

  Ecogenomics/GTDBNCBI#29 · Filter by author donovan-h-parks opened on Feb 9, 2016
  2

• Inherit flags on CLI interface

  Ecogenomics/GTDBNCBI#28 · Filter by author donovan-h-parks opened on Feb 7, 2016

• Database and file structure integrity test

  Ecogenomics/GTDBNCBI#20 · Filter by author donovan-h-parks opened on Oct 30, 2015

• PfamSearch and TigrfamSearch to GenomeTk project

  Ecogenomics/GTDBNCBI#19 · Filter by author donovan-h-parks opened on Oct 30, 2015

• Respect provided called genes file when users add a genome

  Ecogenomics/GTDBNCBI#17 · Filter by author donovan-h-parks opened on Oct 30, 2015

• Flag is needed to indicate missing markers in aligned_markers table

  Ecogenomics/GTDBNCBI#14 · Filter by author donovan-h-parks opened on Oct 26, 2015

• Ownership of genomes and other files in GTDB

  Ecogenomics/GTDBNCBI#11 · Filter by author donovan-h-parks opened on Oct 21, 2015

• Custom labels for genome and marker lists

  Ecogenomics/GTDBNCBI#9 · Filter by author donovan-h-parks opened on Oct 21, 2015

• Check uniqueness of NCBI assembly identifiers

  Ecogenomics/GTDBNCBI#8 · Filter by author donovan-h-parks opened on Oct 21, 2015

• Translation table

  Ecogenomics/GTDBNCBI#7 · Filter by author donovan-h-parks opened on Oct 20, 2015

• Universal marker set

  Ecogenomics/GTDBNCBI#6 · Filter by author donovan-h-parks opened on Oct 20, 2015

• Proper handling of removed/deleted genomes

  Ecogenomics/GTDBNCBI#3 · Filter by author donovan-h-parks opened on Oct 20, 2015