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Hi
Thanks for a great tool. Great to be able to process the output files of kraken without knowing all of the TAXIDs and how they are linked together.
Have you considered making extract_kraken_…
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Hi,
We applied Centrifuge to our full-16S rRNA reads sequenced with the MinION. While the results look good in general, we run into problems when comparing Kraken2 and Centrifuge classifications w…
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Hello
This is a user of Kraken2.
PlusPF database was downloaded in 'https://benlangmead.github.io/aws-indexes/k2' , and the taxonomy information were installed using `kraken2-build --download-taxon…
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Hi,
I would love to clean human contaminated sequences from the GTDB bacteria and archaea (r95) and NCBI viruses and fungi, as classifications are being badly affected in some samples of mine with …
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@matentzn to extend this query:
https://github.com/Knowledge-Graph-Hub/kg-covid-19/blob/master/queries/sparql/query-03-sars-cov-2-interactors.yaml
We could query the graph for human proteins that …
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There is still something funny going on. I have the latest bracken build in ~/build/Bracken and I have the executables as symlinks in ~/bin. They are in the path. For krakenuniq I am using a conda p…
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Thanks for developing the script and making life easier for scientists!
Can you please tell me if it is possible to give a file with taxaID to the input and to provide the output in a separate file?
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Hello.
When running RoseTTAFold-All-Atom using the following input YAML config file, I observed that the inference code returned a `.pdb` file that contains a predicted protein structure with the f…
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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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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.…