Bovine virus and eukaryotic parasite reference sequence databases and associated metadata (v1.0)

This deposit contains the curated reference sequence databases, accompanying metadata tables, and construction notes used for read-based quantification of viruses and eukaryotic parasites in a metatranscriptomic study of pre-weaned dairy calves sampled across 72 farms in New South Wales, Australia (NCBI BioProject PRJNA1191164). Two databases are provided. The bovine virus reference database was used to quantify viral abundance in both manuscripts by mapping quality-filtered reads with BWA-MEM. It comprises 805 nucleotide sequences representing 157 virus taxa across 21 viral families and orders, and was tailored to the sampled population by combining publicly available bovine virus references (743 sequences from NCBI GenBank) with virus sequences assembled from the metatranscriptomic data generated here (62 sequences), so that quantification reflects the diversity of viruses circulating in the study animals. Diverse taxa (notably rotaviruses, caliciviruses and picornaviruses) were represented by clade-level representatives and consensus references; herpesviruses and poxviruses were represented by curated sets of conserved protein-coding genes rather than complete genomes to limit false-positive mapping. Full construction details are given in the accompanying README. The eukaryotic parasite reference database was used to detect and quantify helminth and protozoan parasites in the enteric manuscript. It comprises 202,099 nucleotide sequences retrieved from NCBI GenBank, with taxonomic scope guided by a previously compiled catalogue of bovine parasites (Ul Abedien et al., 2026; https://doi.org/10.3389/fvets.2026.1788101). A separate non-target reference set of 1,974 sequences (the Bos taurus genome, 1,958 sequences, plus 16 bacterial and other sequences that recurrently produced spurious parasite matches) is provided to identify and remove off-target alignments. Full construction details are given in the accompanying README.