My vote would be yes! But it does have the potential for introducing a potentially strange interdependence between funcscan and funcprofiler. But still, if the goal of this pipeline is to functionally annotate reads, it does seem like one reasonable way to do that is to assemble contigs, annotate them and then (at this stage) align the raw reads back to those annotated contigs.
My vote would be yes! But it does have the potential for introducing a potentially strange interdependence between
funcscanandfuncprofiler. But still, if the goal of this pipeline is to functionally annotate reads, it does seem like one reasonable way to do that is to assemble contigs, annotate them and then (at this stage) align the raw reads back to those annotated contigs.