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I was working with a sample made of 50% universal human reference and 50% a bacterial community reference. I used Bracken to get community composition and it removed millions of human reads and reall…
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I use your tool "Prokka" (version 1.10) with your the default rRNA predictor "Barrnap" mainly for metagenome-annotation (and am very happy with it).
As my metagenomes consist of bacterial as well as …
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Hi,
Would it be possible to get an output that is similar to blastp default output? I am running another program that parses the blastp default output to get top hits.
Here is the example of blast…
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Hi,
I was trying to build a bacterial database following the manual, and I was succesful in downloading the taxonomy with:
kraken2-build --download-taxonomy --db /home/gabaldon/kraken_db_nohuman
…
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Extrapolated from common sequencing targets from the SRA, and sequences that returned false positives during initial database screenings:
- Human genome - integration sites: https://hgdownload.soe.…
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**Is your feature request related to a problem? Please describe.**
Where can I find the command used in the web version for bacterial and fungal antiSMASH versions? At the log file you can see how it…
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12:31:27.687 [INFO] deciding the existence of a reference:
12:31:27.687 [INFO] preset profiling mode: 3
12:31:27.687 [INFO] minimum number of reads per reference chunk: 50
12:31:27.687 [INFO] …
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2024oct1 has fewer gene-protein conflations (19,701,538) than 2024aug18 (21,431,316) and slightly fewer info-content values (3,345,015) than 2024aug18 (3,346,582). We should figure out why this is.
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Hello,
I am trying to build PSSM profiles for DNA sequences. The profile construction ran smoothly. Now I need to calibrate the profile with a database and I really cannot find a way to do that. Ca…
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Hello everyone,
I building GTDB databases to be used along with Kraken2. I was wondering if it was possible to add viral refseq sequences while building kraken2 databases? GTDB consists of archaeal a…