I'd like to calculate the differential abundance of a group of contigs in my assembly and compare the relative mapping of these contigs between samples. Previous papers have used RPKM to calculate summed for values for groups of genes or contigs (eg how many reads mapped to ARGs). In other words, they calculated per-gene or per-contig RPKM values and then summed these in samples and compared these summed values between samples. From my understanding, RPKM has flaws and the RNA-Seq field recommends TPM instead. For this application, what do you folks suggest?