mPUMA workflow. Programs used at each step in the pipeline are shown in red. A. User-defined protocol options for assembly and read-to-operational taxonomic unit (OTU) tracking include gsAssembler for both processes (green arrows), gsAssembler plus Bowtie 2 for read tracking (blue arrows), and Trinity assembly plus Bowtie 2 for read tracking (purple arrows). B. Post-assembly analysis of OTU and abundance data. Gray boxes indicate possible downstream analysis tools for which input is generated by mPUMA. The horizontal broken line indicates the transition from analysis of nucleotide OTU ((nt)OTU) and translated peptide OTU ((aa)OTU). Quality of the assembly can be evaluated by assessing Sensitivity/Specificity (Sn/Sp) of each OTU as defined in . WateredBLAST is a combination of BLAST and Smith-Waterman alignments, described in detail in .