2.6. Bioinformatic Analyses of the Viromes

Raw reads were imported into the CLC Genomics Workbench 6.0.1 program (CLC Bio, Aarhus, Denmark) and trimmed according to their quality score, the presence of ambiguities, and their length (reads shorter than 50 nt were discarded). Trimmed reads were compared to the NCBI non-redundant (nr) protein database using the BlastX algorithm using DIAMOND software [38]. The results were visualized using MEGAN software [39] to see the relative abundances of each sequence present in a given sample. Trimmed paired-reads were then assembled into contigs using the CLC Genomics program following the default settings. Contigs were compared to the NCBI non-redundant protein database using the BlastX algorithm with DIAMOND software [38]. The results were observed using the MEGAN software [39]. The open reading frames (ORFs) present in these contigs were determined by MetaGeneMark according to the default heuristic parameters [40]. Translated ORFs were compared to the NCBI nr database by BlastP using the DIAMOND software, and the results were observed with MEGAN (Supplementary File S1).