For metagenomics data analysis, do you do host read cleaning and then assembling or assembling and then host read cleaning?
is it possible that the host and the microorganisms have the reads which have the identical sequence?
if yes, cleaning and then assembling may cause microorganism read loss while assembling and then cleaning may cause false positive microorganism identification.
is my thinking correct?
is it possible that the host and the microorganisms have the reads which have the identical sequence?
if yes, cleaning and then assembling may cause microorganism read loss while assembling and then cleaning may cause false positive microorganism identification.
is my thinking correct?