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Thanks for writing `taxor` and including useful databases!
What the community (or maybe just me) really wants is a database that covers more of the microbial kingdom, but with the benefit of GTDB f…
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#650 reported problems in Bacteria related to emend. phrases.
Now the emend. clause has been removed from the authorship string, which is ok.
However, the comma between the author list and the year …
aoern updated
4 weeks ago
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There are more than 700 taxa in Bacteria whose 'emend.' authors have been removed in April 2024 edition compared to March edition. This is detected by comparing the downloaded NameUsage.tsv files.
Ho…
aoern updated
1 month ago
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Hi, I am working on analyzing one of the proteins of Group A Streptococcus, the M protein. Given the diversity of M protein with a lots of insertions and deletions, I wonder if I can apply virulign to…
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The following is my code
`kraken2-build --download-library bacteria --db bacteria`
`kraken2-build --download-taxonomy --db bacteria`
`kraken2-build --download-library plant --db bacteria`
`krake…
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When using a profile with multiple ranks as input, the output gives summed up ranks for the higher ranks, e.g.:
```
2 1
1224 0.7
1236 0.3
```
Leads to:
```
@SampleID:
@Version:0.10.0
@R…
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When using [SILVA v138.1](https://zenodo.org/record/4587955/files/silva_nr99_v138.1_wSpecies_train_set.fa.gz) (wSpecies_train_set) I get an error in Derep_and_merge_taxonomy.
* fasta file
```
>…
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There are >600 taxa in Archaea and Bacteria (ITIS) where 'emend.' phrase is duplicated. It is both as the NamePhrase property and as part of the ScientificName property.
In search and browse pages an…
aoern updated
2 weeks ago
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I feel like this type of method would work as a fantastic competitor to bacterial whole genome alignment software such as Mauv/progressiveMauve. Have you tried validating this software with bacterial …
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Dear Kraken2 support team,
How to solve errors in the screenshot?
Error when first try
![9d2e6bdc95c1041714e34e29a8ec892c](https://github.com/DerrickWood/kraken2/assets/155892166/63d0952c-210e-41…