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Hi,
I hope to gain taxonomy info while running taxonkit and csvtk using`-t`, which is helpful for me to import the result into R. But R and excel seems to have trouble importing the result. Some l…
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Is it possible to remove a node (or a list of nodes) and (optionally) all those downstream? I am trying to remove all branches of the taxonomy that are unclassified (e.g. 12908).
Something like (wh…
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### 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
`taxonkit` …
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Hi,
I am using taxonkit lineage, and it works wonderfully so far. But there are a few species it seems not to be finding, despite their presence on the NCBI taxonomy portal.
I am not sure how th…
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Hi, I encontered with a new error in running hecatomb v1.3.2, here is the related log information:
```
15:23:41.923 [WARN] taxid 1965493 was merged into 3070820
15:23:41.923 [WARN] taxid 45219 wa…
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per @mr-eyes -
>I was trying yesterday to generate lineage information and follow the format as in all_genbank_lineages.20200727.csv and I started using taxonkit reformat for that purpose but still…
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In order to use the [OPAL tool](https://github.com/CAMI-challenge/OPAL) for analysis and visualization, it might be useful to convert any supported profiler to [that format](https://github.com/bioboxe…
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### 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 do…
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When I use "taxonkit create-taxdump -K 1 -P 3 -C 5 -O 7 -F 9 -G 11 -S 13 -T 15"
I will get this error: "Error: unknown shorthand flag: 'K' in -K". Is there a way to solve this error?
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Hello, I am trying to see if I can install this software without using conda as I'm trying to develop a toolset that has the option of installing with/without conda.
I can install taxonkit using p…