Viral metagenomics of pig feces and sewage

Samples 1–3 consist of viral-enriched metagenomic DNA extracted from pig feces, while samples 4–5 originate from sewage. Metagenomic DNA was sequenced by Eurofins Genomics using the INVIEW METAGENOME service. Sequencing included standard genomic library preparation followed by paired-end Illumina sequencing (2 × 150 bp), generating a minimum of 10 million read pairs per sample. Raw sequencing reads were processed with the ViPER pipeline (Virome Paired-End Reads) to generate viral contigs (De Coninck et al., 2024). This pipeline applies Trimmomatic (Bolger et al., 2014) to trim low-quality bases and adapters from raw reads, followed by assembling the paired-end reads of 1 %, 10 % and 100 % subsets into contigs using metaSPAdes (Nurk et al., 2017). These contigs were clustered using a combination of BLAST+ (Camacho et al., 2009), and anicalc.py and aniclust.py scripts from the CheckV packages (Nayfach et al., 2021). Contigs larger than 500 bp were retained.