Ecogenomics/GTDBNCBI

Issues

• Possible contaminating 16S rRNA in genome assemblies

  #56 opened 3 years ago by hxg2760
  2

• Field indicating isolate or environmental genome.

  #51 opened 6 years ago by donovan-h-parks
  0

• Change & remove published login details

  #50 opened 6 years ago by katrinleinweber
  2

• Export representatives

  #46 opened 7 years ago by donovan-h-parks
  0

• Additional metadata about marker sets would be helpful

  #45 opened 8 years ago by donovan-h-parks
  1

• Need to reannotate Pfam and TIGRfam for all NCBI genomes

  #43 opened 8 years ago by donovan-h-parks
  0

• Check revised annotation for all type strains

  #44 opened 8 years ago by donovan-h-parks
  0

• Calculating and storing metadata is time consuming

  #29 opened 9 years ago by donovan-h-parks
  2

• File file indicating path to all GTDB genomes

  #24 opened 8 years ago by donovan-h-parks
  5

• Delete aligned markers with no marker sets

  #38 opened 8 years ago by pchaumeil
  1

• Possibility to download SSU sequences

  #40 opened 8 years ago by pchaumeil
  1

• Representative user genomes can be deleted

  #39 opened 8 years ago by pchaumeil
  1

• Representative genomes should never be filtered

  #42 opened 8 years ago by donovan-h-parks
  1

• GenBank genomes without called genes

  #41 opened 8 years ago by donovan-h-parks
  1

• Rename older user genomes.

  #21 opened 9 years ago by donovan-h-parks
  0

• Propagate taxonomic annotations to revised NCBI genomes

  #31 opened 9 years ago by donovan-h-parks
  3

• Automatically annotate new User genomes as Bacteria or Archaea

  #32 opened 9 years ago by donovan-h-parks
  1

• Automatic assignment of GTDB taxonomy for clustered genomes

  #33 opened 9 years ago by donovan-h-parks
  1

• Parallel submission of Genomes generates an error

  #37 opened 9 years ago by pchaumeil
  1

• NCBI versioning in directory structure

  #34 opened 9 years ago by donovan-h-parks
  0

• Trimming columns with insufficient taxa is slow

  #36 opened 9 years ago by donovan-h-parks
  0

• Update User genome taxonomy

  #35 opened 9 years ago by donovan-h-parks
  0

• Pull genome sequence data from GTDB

  #30 opened 9 years ago by donovan-h-parks
  1

• Inherit flags on CLI interface

  #28 opened 9 years ago by donovan-h-parks
  0

• Need gtdb_cluster_size and gtdb_clustered_genomes fields in metadata_view table

  #27 opened 9 years ago by donovan-h-parks
  1

• Viewing user marker sets if not currently implemented

  #26 opened 9 years ago by donovan-h-parks
  1

• Delete genomes using genome list IDs

  #25 opened 9 years ago by donovan-h-parks
  1

• GenBank genomes without annotations may be annotated in RefSeq

  #10 opened 9 years ago by donovan-h-parks
  1

• Relative paths to NCBI and user genomes

  #1 opened 9 years ago by donovan-h-parks
  1

• Help menu should separate out required and optional parameters

  #23 opened 9 years ago by donovan-h-parks
  1

• Remove marker set

  #16 opened 9 years ago by donovan-h-parks
  1

• Unknown temporary gene file created by prodigal

  #22 opened 9 years ago by donovan-h-parks
  1

• Genome contains duplicate sequence: delete!

  #15 opened 9 years ago by donovan-h-parks
  1

• Clean-up partial genomes if adding a new genome fails

  #18 opened 9 years ago by donovan-h-parks
  1

• Database and file structure integrity test

  #20 opened 9 years ago by donovan-h-parks
  0

• PfamSearch and TigrfamSearch to GenomeTk project

  #19 opened 9 years ago by donovan-h-parks
  0

• Respect provided called genes file when users add a genome

  #17 opened 9 years ago by donovan-h-parks
  0

• Flag is needed to indicate missing markers in aligned_markers table

  #14 opened 9 years ago by donovan-h-parks
  0

• Generate metadata for new genomes

  #2 opened 9 years ago by donovan-h-parks
  1

• Additional CheckM statistics

  #13 opened 9 years ago by donovan-h-parks
  1

• Tools.runMultiProdigal() in AddManyFastaGenomes() is fixed at 2 processes

  #12 opened 9 years ago by donovan-h-parks
  1

• Ownership of genomes and other files in GTDB

  #11 opened 9 years ago by donovan-h-parks
  0

• Custom labels for genome and marker lists

  #9 opened 9 years ago by donovan-h-parks
  0

• Check uniqueness of NCBI assembly identifiers

  #8 opened 9 years ago by donovan-h-parks
  0

• Logging framework

  #4 opened 9 years ago by donovan-h-parks
  1

• Versioning

  #5 opened 9 years ago by donovan-h-parks
  1

• Translation table

  #7 opened 9 years ago by donovan-h-parks
  0

• Universal marker set

  #6 opened 9 years ago by donovan-h-parks
  0

• Proper handling of removed/deleted genomes

  #3 opened 9 years ago by donovan-h-parks
  0