I have nanopore data that has been classified using centrifuge classifier using the NCBI database (nodes.dmp and names.dmp). I would like to try to analyse with QIIME2. I have converted the data to a biom and managed to import and merge in QIIME2 along with taxonomy. I am unsure how to generate a tree file from the files i have, as i don’t have a rep-seqs.qza -is this possible from the data i have?
No: without sequences, you cannot make an alignment/build a tree. If you figure out a solution for making a tree outside of QIIME 2, then you will be able to import that tree (if it is in newick format) into QIIME 2.
But you can do almost everything QIIME 2 has to offer without a tree: just use non-phylogenetic methods (e.g., run core-metrics instead of core-metrics-phylogenetic for alpha and beta diversity estimates).
Good luck!
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