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Hi! Thanks for developing this tool!
It seems that with Kraken2's "use-names" parameter, which replaces the taxID column with the scientific name and the taxID in parentheses, the filter commands c…
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Hello everyone,
I building GTDB databases to be used along with Kraken2. I was wondering if it was possible to add viral refseq sequences while building kraken2 databases? GTDB consists of archaeal a…
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**Hi, I updated the Hecatomb to the newest version 1.3.0 the day you released it. Unfortunately, it seems that there are some bugs when I run with the command `hecatomb test`, and I have noticed that …
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I need to make a way to build the taxonomy from the NCBI base taxonomy and just have the diff. From there, build a fresh taxonomy. So:
repo changes
1) Create new diff files for `nodes.dmp` and `…
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Hello, I keep having this error when I try to run the pipeline:
```
Traceback (most recent call last):
File "/home/miniconda3/envs/viper/bin/viper_cluster.py", line 21, in
from viper_clus…
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Our framework must be able to provision every tool as either Conda package or (docker) container. At the moment, taxidtools is only available on conda-forge. This means not container is available.
…
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Thanks for the great tool. I'm currently using it like so, based on the wiki:
$ taxonkit lineage taxids.txt | taxonkit reformat -I 1 -t -r NA -R 0 | csvtk -H -t cut -f 1,3 | csvtk -H…
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when trying to add NCBI taxonomy information while running in nucleotide mode (`-z`), it doesn't seem to be pulling the taxid info, as these messages are popping up and there is no tax added in the ou…
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We are getting closer to being able to separate out the lineage stuff from the revindex stuff in LCA, so we could envision combining searches on signatures and SBTs with taxonomic reporting (where ava…
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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
`echo "Sa…