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shenwei356
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taxonkit
A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
https://bioinf.shenwei.me/taxonkit
MIT License
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[Question] Get all species-level taxon ids for organism
#49
jolespin
closed
2 years ago
3
About the special taxonID search
#48
hansir8
closed
3 years ago
2
Update benchmarks
#47
apcamargo
opened
3 years ago
0
How to Extract GenBank 15-taxon format abbreviated lineage
#46
yxj17173
opened
3 years ago
0
Convertion between taxonomic profiling tables with different taxonomy dump file versions?
#45
shenwei356
closed
2 years ago
2
Can I filter taxids using a set of taxids?
#44
Lix1993
closed
3 years ago
2
Can I get kingdom using taxonkit?
#43
Lix1993
closed
3 years ago
2
Taxon taxid reassigned with reformat
#42
standage
closed
3 years ago
11
R bindings for taxonkit?
#41
johanneswerner
closed
3 years ago
4
Unsure about usage of --pseudo-strain
#40
standage
closed
3 years ago
3
reformat: add placeholder for strain?
#39
shenwei356
closed
3 years ago
1
Difference between `--list-order` and `--list-ranks` unclear
#38
standage
closed
3 years ago
3
Possible bug with taxonkit filter --black-list
#37
standage
closed
3 years ago
12
Unnecessary stdin check for taxonkit filter?
#36
standage
closed
3 years ago
4
Inconsistent "taxonkit reformat" output for 446045
#35
standage
closed
3 years ago
3
accession numbers not found
#34
srosales712
closed
3 years ago
1
Refactor: daemon + IPC
#33
shenwei356
closed
3 years ago
1
filtering ranks
#32
shenwei356
closed
3 years ago
11
taxonkit reformat omits species for some species taxids
#31
Shellfishgene
closed
4 years ago
2
JSON output is malformed when running `taxonkit list`
#30
standage
closed
4 years ago
4
duplicate taxid from name2taxid
#29
slaperriere
closed
4 years ago
5
[ERRO] lineage-field (2) out of range (1)
#28
nick-youngblut
closed
4 years ago
1
Why require delnodes.dmp and merged.dmp?
#27
nick-youngblut
closed
4 years ago
5
no lineage info when using custom nodes+names dmp
#26
nick-youngblut
closed
4 years ago
2
how to use taxid-changelog
#25
Phylloxera
closed
4 years ago
4
taxid-changelog bug: 10842
#24
shenwei356
closed
5 years ago
2
taxonkit taxid-changeloge: order error of changes in one taxid
#23
shenwei356
closed
5 years ago
0
new cmd: taxid-changelog
#22
shenwei356
closed
5 years ago
0
autocompletion inside Tmux
#21
matrs
closed
5 years ago
0
Ranks of interest for taxonkit lineage
#20
johanneswerner
closed
5 years ago
4
no taxonomy for "1458427"
#19
nick-youngblut
closed
5 years ago
3
Adding and removing nodes
#18
lskatz
closed
5 years ago
2
$TAXONKIT_DB variable for file locations?
#17
tseemann
closed
5 years ago
2
Export newick tree?
#16
boulund
closed
5 years ago
1
Now in Brew
#15
tseemann
closed
5 years ago
4
taxonkit reformat erro :panic: runtime error: invalid memory address or nil pointer dereference
#14
wfgui
closed
5 years ago
4
add installation script for unix machines
#13
IsmailM
closed
5 years ago
1
citation
#12
IsmailM
closed
5 years ago
4
line-buffered output
#11
tolot27
closed
5 years ago
2
obsolete taxid check
#10
msaavedrat
closed
4 years ago
6
taxonkit Synonyms
#9
msaavedrat
closed
5 years ago
0
output taxid for certain rank or complete lineage
#8
tolot27
closed
6 years ago
13
`taxonkit lineage` stalls if taxID = 1
#7
nick-youngblut
closed
6 years ago
1
format options in lineage command
#6
tolot27
closed
6 years ago
5
reformat should support tab characters in format string
#5
tolot27
closed
6 years ago
1
No output for leaf nodes of the taxonomy
#4
ialbert
closed
6 years ago
7
Taxon ID instead of names in lineage
#3
AsmaTahir
closed
7 years ago
2
Functionality request
#2
dawnmy
closed
7 years ago
0
There are so many ranks
#1
shenwei356
closed
5 years ago
5
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