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I am working mostly with bacteria, and especially with uncultured bacteria many ranks appear that have the taxonomy rank _no rank_. Is it possible to define the ranks that I want to get back? I am thi…
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Hey,
Cool tool - have u published this? How should we cite this in our paper?
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@dfornika I'm running: `kraken2-build --download-taxonomy --db path/to/db`, and I'm getting the following error: `Downloading nucleotide est accession to taxon map...rsync: error while loading shared…
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```
And copy "names.dmp" and "nodes.dmp" to data directory: "$HOME/.taxonkit".
```
We use taxonkit on a shared server with many users.
Would you be able to honour an env variable like `$TAXONK…
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I made this work:
```
brew install brewsci/bio/taxonkit
```
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OMG, so many ranks:
```
class
family
forma
genus
infraclass
infraorder
kingdom
no rank
order
parvorder
phylum
species
species group
species subgroup
subclass
subfamily
subgenus
su…
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**hello,
I've been having some problems lately when using the latest version:**
```
$ taxonkit list --ids 2,4751,13776,10239 --indent "" -j 8 > bac_fun_arc_vir_taxids.txt
$ taxonkit lineage ba…
wfgui updated
6 years ago
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Currently, taxonkit uses xopen fully buffered output writers. Would it be possible to use at least a line-buffered writer? Grep does this by an additional parameter `--line-buffered`.
The rationale b…
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Like the format string in `reformat`, it would be interesting to have placeholders for the taxids of the available ranks.
Most useful for downstream analyses and visualization, i.e. of metagenomic da…
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I'm using `taxonkit` v0.2.0 (installed via bioconda), and I was running `taxonkit lineage` on the "hits" file generated by `centrifuge`. `taxonkit lineage` would very quickly write out taxonomies for …