I'm very new here, and was forced to shift to writing a bioinformatics dissertation because almost all the wet-labs in my country are closed. I am absolutely clueless about how this works and am still studying basic Python/R in the mean time. That being said, I need help designing a workflow for the specific reason of comparing resistance gene abundance between multiple samples of soil.
Would bowtie2 or blastn be more suitable for my needs? Would I need to assemble the data from the Illumina sequencer before alignment?