What does "assembly-level" classification mean?

Question

[psun]

Hello,

I am quite new to metagenomics. I have been looking at different classifiers and had a question regarding one of the terms I have come across when reading papers that evaluate classifiers. What does "assembly-level" classification mean? I understand genus-level classification and species-level classification but am not sure what "assembly-level" classification is referring to.

For context, here is the quote from the reference:

"TaxSBP supports one level of specialization after the leaf nodes of the tree, making it possible to further cluster sequences by strain or assembly information that is not directly contained in the NCBI Taxonomy database."

Thank you.

Answer 1

[h.mon]

Here is one relevant paper about this proposition:

Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records

From what I understand, until recently prokariotic strains were assigned a "strain taxid". With the growth in number of deposited genomes, this practice became unfeasible, and the authors of the above paper suggest the strain taxid should be replaced by the BioProject, BioSample and Assembly records metadata. In theory, this would allow an even more finer-grained classification then the strain-level classification.

[psun]

Thank you for the link and for the clarification. It makes much more sense to me now.