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Is it possible to generate a graphical representation of a taxdump?
Most taxdumps are huge and impractical to represent graphically but, sometimes when testing, users work with reduced taxdumps tha…
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I cannot seem to figure out if this is an issue or not. I'm using kaiju-makedb in cluster. It required taxdump that is why I added that file in the directory. I also did md5sum for the file but it did…
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Hello!
I'm trying to download progenomes database and see that:
Downloading taxdump.tar.gz
.listing [ …
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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
* [x] des…
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I just worked my way through the download_taxonomy.sh script and was wondering why the file taxdump.tar.gz isn't removed after it has been extracted. It's removed downstream if the clean_db.sh script …
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Taxdump.tar.gz is downloaded to a user directory, it contains the names and nodes files.
```
Downloading http://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz to /home/adam/.local/var/lpi/taxdump.…
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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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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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The `genus` and `species` fields can be checked against local `taxdump/genus.txt` and `taxdump/species.txt`.
(a) write generic TaxdumpLookup
(b) integrate it to `ami-phylo`
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Hello Thank you for your nice work.
I downloaded GTDB taxa to utilize it for kraken database. (the taxonomy files you've created)
I utilized GTDBr214.1 taxdump files.
I just found out one spec…