metagenomic of swimming pool water: Shanghai
Sequencing was performed on the Illumina Novaseq 6000 platform, generating 150 bp paired-end reads. Fastp (v 0.20.1) was used to remove adapters and filter out low-quality bases and reads containing N bases (ambiguous bases) from the raw sequencing data. MEGAHIT (v 1.2.9) was employed for metagenomic assembly. Prodigal (v 2.6.3) was used to predict ORFs in the assembled scaffolds, which were then translated into amino acid sequences. MMSeqs2 (v 13.45111) was used to construct a non-redundant gene set from the predicted genes across all samples, with clustering parameters set at 95% sequence identity and 90% coverage. The longest gene in each cluster was selected as the representative sequence of the gene set. After obtaining the representative sequences, Salmon (v 1.8.0) was used to align the clean reads of each sample to the non-redundant gene set (95% identity) and calculate gene abundance in the corresponding samples. Genes with fewer than 2 reads across all samples were removed to obtain the final Unigene. The abundance of each gene was calculated based on the number of aligned reads and gene length. Taxonomic annotation was performed using the NCBI non-redundant database (NR)