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hi Mike,
I met the same as Issue #22. I install krona with mamba. Then I successfully updated the Kron database using the following code.
KRONA_DIR=$( which python | sed 's/bin\/python/opt\/kro…
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I built a taxdump using a custom taxonomy with the command:
`taxonkit create-taxdump genome_taxonomy.tsv -A 1 -O out--force`
A few of the accessions in `genome_taxonomy.tsv` start with "Sp_" and I…
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### reformat 格式选择如下
Output format can be formated by flag --format, available placeholders:
{k}: superkingdom
{p}: phylum
{c}: class
{o}: order
{f}: family
{g}: genus
…
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### Prerequisites
- [x] `taxonkit v0.12.0`
- [x] read the [usage](http://bioinf.shenwei.me/taxonkit/usage/)
### Describe your issue
I want to create a simplified taxonomy of all fungi. It se…
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Genomes in MGV and GPD were assembled from shotgun metagenomic data (MAG). Though they are clustered into species, there are no official TaxIds available to show their relationship.
A new command …
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Hi
I got the following error, when I'm trying to do the filtering from the tutorial (section 3a method 3)
rush: invalid option -- 'j'
Can you help me fix this?
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Hello developer, I'm trying to run Autometa.sh bash script on a HPC server.
I made a coassembly of environmental paired reads libraries, produced a bam file per each sequencing set, merged those…
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### Prerequisites
- [x] `taxonkit v0.12.0`
- [x] read the [usage](http://bioinf.shenwei.me/taxonkit/usage/)
### Describe your issue
I have a few issues with using `taxonkit create-taxdump` a…
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### What happened?
Hello,
I am encountering a bug with the latest versions of the workflow when aggregating kraken reports with bracken. Something is wrong with the parsing of the kraken report …
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Dear Dr. Shen,
I have a question about taxdump in KMCP documentation.
The documentation mentioned:
```
# taxid mapping files, multiple files supported.
taxid_map=gtdb.kmcp/taxid.map,refseq-viral.…