Hello all, I have got all my clear, putative viral/bacterial sequences from a metagenomic sequence file. Now I am not able to understand how to proceed with that.
I used bowtie2 tool for aligning my sequences to reference db, and retrieved my sequences, in article which I am referring Skoporov et al., 2019 it says they used phyloseq and ggplot2, etc R packages for alpha and beta diversity and phylogeny identification. But the problem is I am not able to consturct OTU table for my sample plus I was thinking whether it is necessary to make otu table or there is any other tools/ toolkit to do the work.??