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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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profile2cami not working as expected
#99
paulzierep
opened
3 days ago
6
Exclude nodes from the taxonomy
#98
fgvieira
opened
1 month ago
2
Filter of ranks without order
#97
alvanuffelen
opened
2 months ago
5
Extracting taxids for each desired taxonomic ranks into their own columns
#96
charlesfoster
closed
2 months ago
2
[Question] Graphical representation of taxdumps
#95
fgvieira
opened
3 months ago
2
convert taxdump from IMG/VR metadata
#94
fgvieira
closed
3 months ago
1
[Feature] taxonkit list from taxon name
#93
fgvieira
opened
3 months ago
3
Missing ranks for GTDB genomes with duplicate names at different ranks
#92
donovan-parks
closed
4 months ago
8
Discrepancy GTDB website and taxdump changelog
#91
danielpodlesny
opened
4 months ago
5
some taxid that have taxonomy on ncbi but taxonkit not found or not complete
#90
weiguanyue
closed
4 months ago
1
Include LCA queries in output even when all taxids are skipped
#89
standage
closed
7 months ago
3
[Feature Request] Fuzzy name searching with name2taxid
#88
jolespin
opened
8 months ago
3
Search equivalent names with name2taxid?
#87
alvanuffelen
closed
3 months ago
2
taxonkit equivalent of diamond blastx plus megan blast2lca
#86
avilella
opened
10 months ago
3
ranks skipped in certain GTDB lineages
#85
ggavelis
closed
10 months ago
2
Filter duplicate taxIDs by order/class?
#84
philippbayer
closed
11 months ago
3
kraken2 report to mpa with counts
#83
motroy
closed
11 months ago
2
How to add the corresponding taxonomic level prefix based on the taxonomy name?
#82
YeGuoZJU
closed
10 months ago
6
An error occurs when running the latest version
#81
weiguanyue
closed
1 year ago
5
Possible issue with `filter --save-predictable-norank` and merged taxids
#80
standage
closed
1 year ago
2
taxonkit reformat taxid 0 not found
#79
Krasnopeev
closed
1 year ago
2
taxid-changelog: support gzip-compressed dump files for saving space
#78
shenwei356
closed
1 year ago
1
Placeholder for Clade rank (reformat)
#77
poursalavati
closed
1 year ago
4
"Error: Invalid taxonomic rank: realm" when making Diamond db of IMG/VR dataset
#76
poursalavati
closed
1 year ago
5
taxonkit lca gives error `[ERRO] bufio.Scanner: token too long' sometimes
#75
taylorreiter
closed
1 year ago
4
Feature request: accession2taxid
#74
stas-malavin
closed
1 year ago
2
build(deps): bump golang.org/x/sys from 0.0.0-20210510120138-977fb7262007 to 0.1.0
#73
dependabot[bot]
closed
1 year ago
1
Feature request: report specific lineage ranks
#72
soungalo
closed
1 year ago
1
modification of the dmp files?
#71
nick-youngblut
closed
1 year ago
2
Error with makeblastdb using GTDB taxonkit create-taxdump taxid.map
#70
BenjaminJPerry
closed
1 year ago
4
Error rush: invalid option -- 'j'
#69
Metag3nOmics
closed
1 year ago
12
Error in list method
#68
Maryam-Haghani
closed
1 year ago
10
Create-taxdump not generating subspecies
#67
Lucas-Maciel
closed
1 year ago
4
panic: runtime error: index out of range [4] with length 4
#66
Summer0lhl
closed
1 year ago
1
Sequence names starting with "Sp_"
#65
snayfach
closed
1 year ago
5
taxonkit reformat 如何显示kingdom 信息
#64
zhaolei6116
closed
1 year ago
4
Trouble creating taxdump after using reformat
#63
Midnighter
closed
1 year ago
6
Is it expected to have different output from reformat depending on whether the input are only tax IDs or a lineage table?
#62
Midnighter
closed
1 year ago
2
create-taxdump: accepts arbitrary ranks. #60
#61
shenwei356
closed
2 years ago
0
create-taxdump: accepts arbitrary ranks
#60
shenwei356
closed
2 years ago
1
taxids created with `create-taxdump` skip numbers
#59
apcamargo
opened
2 years ago
2
Make create-taxdump parse classes correctly
#58
apcamargo
closed
2 years ago
0
`create-taxdump` ignores the class rank
#57
apcamargo
closed
2 years ago
5
TODO: new command to create taxdump files for MAG genome collections
#56
shenwei356
closed
2 years ago
15
When converting 'taxid' into full taxonomy from prot.accession2taxid , the program terminated after an error is reported
#55
Neal050617
closed
2 years ago
10
Taxonkit Bash-completion terminal error
#54
divya1srv
closed
2 years ago
1
[Question] How to get specific taxonomic fields (not full taxonomy string) from a list of taxon identifiers?
#53
jolespin
closed
2 years ago
5
"out of range" error for Reformat on long taxonomic strings
#52
mycowx
closed
2 years ago
2
Taxonkit list tabular output
#51
mweberr
closed
2 years ago
2
fixes typos with strain
#50
tolot27
closed
2 years ago
1
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