I am looking for instructions on creating a custom-made kraken2 catalogue from the sequences of my choice and the corresponding phylogenetic tree in newick notation.

I will appreciate an input on whether/how it can be done. The prescription provided in the kraken2 manual seems to assume that sequences and phylogeny originate from the NCBI. Struo2 extends this to GTDB sequences. However, in my case the sequences are collections of concatenated genes (i.e., not full genomes), provided by a third party.

Remark: (in response to comments) I don't need to work with newick format - I have the tree in newick format. So converting it to dmp might be a part of the answer.

  • $\begingroup$ Newick has a lot of different ways to represent data, so it's helpful to know specifically what your input data looks like. When asking a question, it's helpful to provide both example input and example output. You've provided good information on the output side through the link, but no information on the input format. $\endgroup$
    – gringer
    Apr 19, 2023 at 19:54
  • $\begingroup$ @gringer Does kraken2 need this information? The question is not about solving my particular research problem (which is off topic?), but about creating a kraken2 catalogue from sequences and phylogeny, other than those readily provided by NCBI or GTDB (via Struo). [contd.] $\endgroup$
    – Roger V.
    Apr 20, 2023 at 8:11
  • $\begingroup$ You seem to be suggesting, that, once phylogeny is converted to dmp format, the problem is easily resolved - if that's the case, then state this explicitly, specify the tools for converting newick to dmp, and the minimal information that a newick tree should contain for creating a meaningful kraken2 catalogue. The would make for a nice answer, and useful for other users that stumble on the same problem. $\endgroup$
    – Roger V.
    Apr 20, 2023 at 8:11
  • $\begingroup$ I'm not trying to give answers, just clarify the question. My comments are more generally applicable to all questions on this site: a good question for StackExchange has a specific, well-defined input, and a well-defined output. All I'm trying to do is make sure that this question will receive good answers. $\endgroup$
    – gringer
    Apr 20, 2023 at 20:20
  • $\begingroup$ Yes, phylogeny is important. Kraken2 is a phylogenetic mapper, and uses the tree structure to work out the best match when it cannot be assigned reliably to a single species. $\endgroup$
    – gringer
    Apr 20, 2023 at 20:23


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