Fig. 1

ResCap analysis workflow. Processed reads are mapped against the reference database. SAM files are parsed to extract the reads unequivocally mapped and those ambiguously mapped to determine the genes unequivocally detected and to form the allele network. The allele network is built using all the study’s SAM files. The MGCs determined from the allele network were used to perform the statistical analysis of abundance and diversity. Finally, a differential analysis was performed with the abundance data