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The blast taxdb is a .tar.gz and the NCBI taxdump is a .zip. There's a .tar.gz available for the latter, so maybe we should just use the same for both? That way we can reuse the same process to extrac…
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Hi @BenLangmead thanks for providing these convenient databases (as well as your excellent open-source software).
First let me explain what we're trying to do and what we've tried so far. Then I'll…
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`taxopy.TaxDb` should be able to download specific snapshots from the [`taxdump_archive`](https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/).
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Hi,
I really like this project!
Do you also archive all the historical taxdump *.dmp files?
If you are interested, I could send you some older files from before 2014-08-01.
I have files from t…
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As far as I can tell from reading the docs & paper on `taxa`, the package cannot directly import from taxdump files. This would be helpful for importing custom taxdump files created from non-NCBI taxo…
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When I use "taxonkit create-taxdump -K 1 -P 3 -C 5 -O 7 -F 9 -G 11 -S 13 -T 15"
I will get this error: "Error: unknown shorthand flag: 'K' in -K". Is there a way to solve this error?
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Dear mmseq2 team
I am trying to create taxonomy database for ncbi nr data base. First I downloaded nr.fa, taxdump and prot.accession2taxid. Then I ran the below commands
mmseqs createdb nr.fa nr…
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The NCBI taxdump contains ca 600K records, looking like:
```
9 | Buchnera aphidicola | | scientific name |
9 | Buchnera aphidicola Munson et al. 1991 | | synonym |
10 | "C…
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I used sequencing data to align with Bowtie2 to the GTDB database, and then I used the gtdb_to_taxdump.py and acc2gtdb_tax.py scripts to generate name, nodes, and acc2tax files. However, I encountered…
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I used sequencing data to align with Bowtie2 to the GTDB database, and then I used the gtdb_to_taxdump.py and acc2gtdb_tax.py scripts to generate name, nodes, and acc2tax files. However, I encountered…