taxonkit

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taxids created with `create-taxdump` skip numbers

2

When you create a taxdump using `create-taxdump` (ICTV taxonomy, for example), the taxids "skip" some numbers. For example: ``` $ head ictv-taxdump/names.dmp 1 | root | | scientific name |...

apcamargo

I just released version 0.6.0 of taxopy where the only change is that taxids are now encoded as integers instead of strings. The code is now faster and uses less...

apcamargo

### Prerequisites - [ ] make sure you're are using the latest version by `taxonkit version` - [ ] read the [usage](http://bioinf.shenwei.me/taxonkit/usage/) ### Describe your issue For examples, human complete...

yxj17173

Error in list method

8

Hi, I am using _**list**_ command to get the sub-trees for 3 taxa of _[11050, 11103, 11108]_, the result is different for different orders of these taxa. i.e.: When I...

Maryam-Haghani

Create-taxdump not generating subspecies

3

Hi, I'm trying to use taxonkit create-taxdump but I have two questions: 1) I'm using the following command but all my "accession" names are being assigned as "no rank "...

Lucas-Maciel

panic: runtime error: index out of range [4] with length 4

1

hello，when using any taxonkit commond, got following errors. ` $taxonkit list --ids 9606 --indent "" panic: runtime error: index out of range [4] with length 4 goroutine 17 [running]: github.com/shenwei356/taxonkit/taxonkit/cmd.stringSplitN({0xc004423c20,...

Summer0lhl

[Feature Request] Fuzzy name searching with name2taxid

3

### Prerequisites - [x] make sure you're are using the latest version by `taxonkit version` - [x] read the [usage](http://bioinf.shenwei.me/taxonkit/usage/) ### Describe your issue * [x] describe the problem Similar...

jolespin

Discrepancy GTDB website and taxdump changelog

5

### Prerequisites - [x] make sure you're are using the latest version by `taxonkit version` - [x] read the [usage](http://bioinf.shenwei.me/taxonkit/usage/) ### Describe your issue * [x] describe the problem Thanks...

danielpodlesny

taxonkit equivalent of diamond blastx plus megan blast2lca

3

Hi, I've followed the methods section in this paper: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1299-7 To generate `diamond blastx` hits from short-read WGS data, and I wanted an equivalent to megan/tools/blast2lca which it seems taxonkit...

avilella

Filter of ranks without order

5

### Prerequisites - [x] make sure you're are using the latest version by `taxonkit version` - [x] read the [usage](http://bioinf.shenwei.me/taxonkit/usage/) ### Describe your issue In the documentation, it mentions: >...

alvanuffelen