Water_RiverPE333
Sequence analysis was performed with our bioinformatic pipeline as described previously with slight modifications . First, quality filtering and trimming (> Q30 quality score) was performed on all the reads of the 16S rRNA V1 hypervariable region using Sickle version V1.2 software. Second, read error correction was performed using the BayesHammer module within SPAdes V2.5.0 software to obtain high-quality assemblies. Third, paired-end reads were merged (overlap length 50 bp) using PANDAseq v2.11 software with a simple_Bayesian read merging algorithm. After overlapping paired-end reads, merged reads were dereplicated, sorted, and filtered chimaeras using the GOLD SILVA reference dataset, and singletons were removed by using the VSEARCH version 2.3.4 tool [44]. Merged paired-end filtered reads were clustered in operational taxonomic units (OTUs) using the VSEARCH software at 97% identity followed by a decontamination step by mapping OTUs against the host (Salmo salar) reference genome (available on NCBI) DNA using the BWA aligner implemented in the DeconSeq v0.4.3 tool. Taxonomic assignment of OTUs was achieved using the Nave Bayesian Classifier implemented in the QIIME 2 platform using the SILVA 132 database. Phylogenetic trees of OTUs were generated using FastTree software after using MAFFT for multiple sequence alignment. The resultant OTU table was converted to a biological observation matrix (BIOM) format for the post-OTU statistical analysis.