A total of 1,918 contigs, 8.43% of those annotated, had homology with the main groups of putatively pathogenic organisms such as viruses (47 hits), bacteria (1,126 hits), protozoa (341 hits) and fungi (404 hits). Figure 9 displays the taxonomic classification of these sequences and Table 3 summarizes a list of the known bivalve pathogens found in our results.