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FOI-Bioinformatics
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flextaxd
FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )
GNU General Public License v3.0
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flextaxd error: "ValueError: not enough values to unpack (expected 2, got 1)"
#70
morien
opened
7 months ago
2
Update ReadTaxonomyCanSNPer.py
#69
davve2
opened
1 year ago
0
various fixes
#68
jaclew
closed
1 year ago
0
added --purge_database functionality to purge a FTD from genomes that…
#67
jaclew
closed
1 year ago
0
Krakenuniq databases can now be made from a FTD-database + minor fixes
#66
jaclew
closed
1 year ago
0
Various fixes, primarliy related to downloading genomes
#65
jaclew
closed
1 year ago
0
Various fixes, primarliy related to downloading GTDB genomes
#64
jaclew
closed
1 year ago
0
fixed so genomes missing in flextaxd-database are downloaded from...
#63
jaclew
closed
1 year ago
0
fixed issue where flextaxd-create would give an error if a "logs/"-di…
#62
jaclew
closed
1 year ago
0
Include database dmp in kraken2 build command
#61
davve2
closed
1 year ago
0
Fixed rank-issue on import from --mod_file
#60
jaclew
closed
1 year ago
1
Added a function that naively attempts to rename a node. This needs e…
#59
jaclew
closed
1 year ago
0
Implemented escape from poor recursive behaviour that resulted in RecursionError
#58
jaclew
closed
1 year ago
0
Fixed building of Newick-tree in visualization that previously lacked…
#57
jaclew
closed
1 year ago
1
[Question] Does taxonomy exported from flextaxd only contained species with genome available in refseq folder? Can I make use of library.fna downloaded via kraken2-build?
#56
zztin
opened
1 year ago
0
Adding a custom seqid2taxid file to the NCBI accession2taxid causes error
#55
MortenEneberg
closed
1 year ago
1
V0.4.3
#54
davve2
closed
2 years ago
0
Name bug issue51 fix
#53
davve2
closed
2 years ago
0
Use of custom genomes retrieved from another databases apart from NCBI and GTDB in FlexTaxD
#52
magibc
closed
2 years ago
5
Create completely custom Kraken2 database
#51
mw55309
closed
2 years ago
5
Krakenuniq "Unknown options: skip-maps"
#50
MortenEneberg
closed
2 years ago
2
Flextaxd - test database inspect file has no genome names
#49
MortenEneberg
closed
2 years ago
13
Flextaxd creates empty kraken db
#48
SilasK
closed
2 years ago
14
Issues with replacing NCBI bacterial and archeal taxonomies with GTDB taxonomies
#47
MortenEneberg
closed
2 years ago
11
TypeError: 'int' object is not iterable
#46
xvtyzn
closed
2 years ago
3
MP style output
#45
davve2
opened
3 years ago
1
Issues with cleaning and merging NCBI+GTDB database
#44
HitMonk
closed
3 years ago
3
Version update v0.4.2
#43
davve2
closed
3 years ago
0
Version update v0.4.1
#42
davve2
closed
3 years ago
0
16s GTDB database: Kingdom taxonomy issue
#41
HitMonk
closed
3 years ago
3
Bugs 20210305
#40
davve2
closed
3 years ago
1
Iss33
#39
davve2
closed
3 years ago
28
Importing trees with unspecified rank levels
#38
davve2
opened
3 years ago
0
Self linked parents
#37
davve2
closed
2 years ago
0
Error message when no gneomes are found
#36
SilasK
closed
3 years ago
1
Using flextaxd to modify the taxonomy without genomes
#35
mw55309
closed
3 years ago
3
Custom genome annotations with "-" sometimes gets lost
#34
davve2
opened
3 years ago
0
Building Kraken2 compatible GTDB only database
#33
HitMonk
closed
3 years ago
35
Updates 202011
#32
davve2
closed
3 years ago
0
Bug on replace
#31
davve2
closed
3 years ago
1
Update README.md
#30
davve2
closed
3 years ago
0
Cano not import name "BadGzipFile"
#29
alienzj
closed
3 years ago
3
Use GTDB genomes (representatives or all) instead of NCBI
#28
davve2
closed
3 years ago
0
Bug fixes 20201029
#27
davve2
closed
3 years ago
0
Visualisation option added, Kraken2 - bug fixed.
#26
davve2
closed
3 years ago
0
Add - to fit bracken names and nodes format
#25
davve2
closed
3 years ago
1
genomeid2taxid of local files does not allow names to be without .fa/.fasta
#24
davve2
closed
3 years ago
0
Version-0.3.2
#23
davve2
closed
3 years ago
0
Non-unique contig names for GTDB
#22
andrewjmc
closed
3 years ago
5
Bug fixes 202010
#21
davve2
closed
3 years ago
0
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