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Metapro is missing the taxid_trees file, or whatever file is supposed to be found in that folder. The lib_downloader.py script seems to have completed successfully, but no file or folder with that nam…
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Hello,
I am using centrifuge to classify metagenomic reads from different environments using nt databse.
For some experiments (e.g., host microbiome, ...), it is very useful to exclude host genome f…
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Hi,
I am evaluating the performance of KrakenUniq with in silicon data. Here is the result:
C 11137_88628 1000047973 201 11137:60 1000047973:1 11137:9 A:31 11137:70
C 1…
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**Describe the bug**
The rabies genome package includes invalid host taxon ids that cannot be fetched as a taxonomy package.
**To Reproduce**
1. Download rabies virus genome package with `da…
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The formatter taxId(), in require-dev fzaninotto/faker ver 1.8.0, is unknown
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when I build nr database ,the error:
```
$ kraken2-build --build --db ~/software/metadb
Creating sequence ID to taxonomy ID map (step 1)...
No preliminary seqid/taxid mapping files found, aborti…
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I have developed a bioinformatics pipeline that processes alignment results generated by minimap2, with an emphasis on minimizing the disk storage and maximizing analysis speed. To achieve this, I opt…
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I used HGTector2 to predict HGTs in my genome, and it classified my genome as "phylum Proteobacteria". The prediction results showed that 318 genes were identified as HGTs, but only 40 of them had a '…
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Strain TaxIDs are [deprecated since 2014](https://www.ncbi.nlm.nih.gov/news/11-21-2013-strain-id-changes/). Sequences which had already been assigned at this level will remain though. This explains wh…
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Hello,
I'm looking to create a custom database to run in Phylosift and keep getting error messages when trying to build the database using The Monkey. I can index the created database, but the taxa …