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Thank you very much for your powerful tools!
I ran into the following error while running the make_kreport.py script.
python make_kreport.py -i P1_S7_L001_R_kraken2.txt -t nt_ktaxonomy -o P1
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Hi, I need to build a custom database for my master thesis, but the problem is that, eventually, if I check the DB with the inspect function, it has "table size" equal to 0.
I followed the document…
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I am hoping for some advice.
basically I want to classify my PE reads to Archaea, Bacteria, Eukaryote and Virus (d: domain with K: kingdom option being optimal) as to get an overview as to the % a…
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Hello everyone,
I was trying to build Krake2 databases with GTDB. However, since GTDB consists of only bacterial and archaeal sequences it would be ideal to build it along with the viral Refseq. Im n…
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In our current invocations in the WDL workflow, we run kraken, and then krona, on a bunch of samples to save on DB staging time and such. Currently, the krona portion is run in a for-loop after kraken…
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Request to update the get-ncbi-data to format the taxon table as it would appear in SILVA. Currently, the scripts populates all ranks regardless of presence in TaxID lineage.
Example of actual:
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I want to use hhblits to make a multiple sequence alignment using only eukaryote sequences. Is there a way to get only the eukaryote sequences from the uniclust database.
:exclamation: Make to chec…
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**Odd BOLD names**
The BOLD checklist dataset contains some thousand "names" which are neither BOLD identifiers nor scientific names. Are they important or could they maybe be removed from the datase…
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I would like to run the seq similarity search against the homo sapien samples in the NR dataset. For that I downloaded the dataset as follows:
`mmseqs databases NR nr tmp`
Then I attempted to f…