issues
search
Ecogenomics
/
GTDBNCBI
The GTDB provides the software infrastructure for working with a large collection of genomic resources. The major goal of this initiative is to provide a phylogenetically consistent taxonomy for archaea and bacteria.
https://gtdb.ecogenomic.org/
GNU General Public License v3.0
9
stars
2
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
feat: migrated code to Python3; removed unused imports; moved checkin…
#57
donovan-h-parks
closed
11 months ago
1
Possible contaminating 16S rRNA in genome assemblies
#56
hxg2760
closed
3 years ago
2
update packaging for conda v2.3.2
#55
aaronmussig
closed
4 years ago
0
python packaging
#54
aaronmussig
closed
4 years ago
0
Added GTDB to SILVA taxonomy summary
#53
aaronmussig
closed
5 years ago
0
Dev pierre
#52
pchaumeil
closed
5 years ago
0
Field indicating isolate or environmental genome.
#51
donovan-h-parks
opened
6 years ago
0
Change & remove published login details
#50
katrinleinweber
closed
6 years ago
2
Dev donovan
#49
pchaumeil
closed
6 years ago
0
multithread branch creation
#48
pchaumeil
closed
6 years ago
0
remove gtdb_taxonomy from metadata_table
#47
pchaumeil
closed
6 years ago
0
Export representatives
#46
donovan-h-parks
opened
7 years ago
0
Additional metadata about marker sets would be helpful
#45
donovan-h-parks
closed
8 years ago
1
Check revised annotation for all type strains
#44
donovan-h-parks
opened
8 years ago
0
Need to reannotate Pfam and TIGRfam for all NCBI genomes
#43
donovan-h-parks
closed
8 years ago
0
Representative genomes should never be filtered
#42
donovan-h-parks
closed
8 years ago
1
GenBank genomes without called genes
#41
donovan-h-parks
closed
8 years ago
1
Possibility to download SSU sequences
#40
pchaumeil
closed
8 years ago
1
Representative user genomes can be deleted
#39
pchaumeil
closed
8 years ago
1
Delete aligned markers with no marker sets
#38
pchaumeil
closed
8 years ago
1
Parallel submission of Genomes generates an error
#37
pchaumeil
closed
8 years ago
1
Trimming columns with insufficient taxa is slow
#36
donovan-h-parks
opened
8 years ago
0
Update User genome taxonomy
#35
donovan-h-parks
opened
8 years ago
0
NCBI versioning in directory structure
#34
donovan-h-parks
closed
8 years ago
0
Automatic assignment of GTDB taxonomy for clustered genomes
#33
donovan-h-parks
closed
8 years ago
1
Automatically annotate new User genomes as Bacteria or Archaea
#32
donovan-h-parks
closed
8 years ago
1
Propagate taxonomic annotations to revised NCBI genomes
#31
donovan-h-parks
closed
8 years ago
3
Pull genome sequence data from GTDB
#30
donovan-h-parks
closed
8 years ago
1
Calculating and storing metadata is time consuming
#29
donovan-h-parks
opened
8 years ago
2
Inherit flags on CLI interface
#28
donovan-h-parks
opened
8 years ago
0
Need gtdb_cluster_size and gtdb_clustered_genomes fields in metadata_view table
#27
donovan-h-parks
closed
8 years ago
1
Viewing user marker sets if not currently implemented
#26
donovan-h-parks
closed
8 years ago
1
Delete genomes using genome list IDs
#25
donovan-h-parks
closed
8 years ago
1
File file indicating path to all GTDB genomes
#24
donovan-h-parks
closed
8 years ago
5
Help menu should separate out required and optional parameters
#23
donovan-h-parks
closed
8 years ago
1
Unknown temporary gene file created by prodigal
#22
donovan-h-parks
closed
8 years ago
1
Rename older user genomes.
#21
donovan-h-parks
closed
8 years ago
0
Database and file structure integrity test
#20
donovan-h-parks
opened
8 years ago
0
PfamSearch and TigrfamSearch to GenomeTk project
#19
donovan-h-parks
opened
8 years ago
0
Clean-up partial genomes if adding a new genome fails
#18
donovan-h-parks
closed
8 years ago
1
Respect provided called genes file when users add a genome
#17
donovan-h-parks
opened
8 years ago
0
Remove marker set
#16
donovan-h-parks
closed
8 years ago
1
Genome contains duplicate sequence: delete!
#15
donovan-h-parks
closed
8 years ago
1
Flag is needed to indicate missing markers in aligned_markers table
#14
donovan-h-parks
opened
8 years ago
0
Additional CheckM statistics
#13
donovan-h-parks
closed
8 years ago
1
Tools.runMultiProdigal() in AddManyFastaGenomes() is fixed at 2 processes
#12
donovan-h-parks
closed
9 years ago
1
Ownership of genomes and other files in GTDB
#11
donovan-h-parks
opened
9 years ago
0
GenBank genomes without annotations may be annotated in RefSeq
#10
donovan-h-parks
closed
8 years ago
1
Custom labels for genome and marker lists
#9
donovan-h-parks
opened
9 years ago
0
Check uniqueness of NCBI assembly identifiers
#8
donovan-h-parks
opened
9 years ago
0
Next