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Hi Wei, have you ever thought of implementing clustering?
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### What happened?
Lines 139 and 140 of **kraken_pipeline.nf**
you are assuming that every OTUs have 2 names, but what about this OTU name?
Severe acute respiratory syndrome coronavirus
fiel…
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### Prerequisites
- [x] make sure you're are using the latest version by `csvtk version`
- [x] read the [usage](http://bioinf.shenwei.me/csvtk/usage/)
### Describe your issue
taxonkit 联合 csv…
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#### IN SHORT:
When names in a lineage are identical (e.g if genus, family, and order are all called 'SpSt-165') those ranks get collapsed in the names.dmp and nodes.dmp files. This results in incomp…
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### Is there an existing issue for this?
- [X] I have searched the existing issues
### Problem description
Hi, thank you for a great tool!
I am getting: AttributeError: 'DataFrame' object has n…
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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
As descri…
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Hello,
Thanks for developing kmcp and for providing detailed documentation. I am running into empty output file after running `kmcp profile` command.
The commands I am using are:
`kmcp comp…
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Dear Dr. Shen,Thank you for such a handy tool！
I have a question. I use `metawrap classify_bins ` to assign taxonomy to genomic bins, and the result show as follow:
> bin.10.fa Bacteria;Bacillo…
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### Prerequisites
Dear teacher, I need to decontaminate the original sequencing data, and the comparison results are outputed by comparing NT database with blastn. But the result of comparison is o…
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The MetaPhlAn output generated by KMCP is not the same as the one generated by MetaPhlAn. In the KMCP output, the taxid column only contains the taxid of the lowest taxonomic rank (e.g. `1224`), while…