benjjneb / dada2

Accurate sample inference from amplicon data with single nucleotide resolution
http://benjjneb.github.io/dada2/
GNU Lesser General Public License v3.0
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Taxonomy assignment, reads alignment and mapping? #1726

Closed marwa38 closed 5 months ago

marwa38 commented 1 year ago

Hey Just kind of confused about terminologies differences between reads alignment and mapping against SILVA for example. When to use any of those terms? DADA2 tutorial presented taxonomy assignment step without mentioning if that is a kind of alignment or mapping if there is differences between both terms? For the phylogenetic tree creation in DADA2 tutorial, DECIPHER have been used and alignment term was used alongside. Thanks Marwa

benjjneb commented 1 year ago

I'm not entirely clear on the question here. If it is the methodology behind assignTaxonomy, that function is a reimplentation of the naive Bayesian classifier method: https://journals.asm.org/doi/full/10.1128/AEM.00062-07

"taxonomic assignment" or "taxonomic classification" would be an appropriate terminology for what the naive Bayesian classifier does.