A multi-source approach for the detection and diversity assessment of avian schistosomes (Trematoda, Schistosomatidae) in freshwater ecosystems

Raw Illumina MiSeq FASTQ files generated for the study "A multi-source approach for the detection and diversity assessment of avian schistosomes (Trematoda, Schistosomatidae) in freshwater ecosystems". The study evaluated and compared three complementary approaches for detecting avian schistosomes in freshwater ecosystems: (i) eDNA metabarcoding of environmental water samples targeting free-living parasite stages and extracellular DNA, (ii) metabarcoding of snail tissues to detect prepatent infections, and (iii) conventional parasitological examination of snail hosts. The dataset comprises ITS1–5.8S rDNA metabarcoding sequences obtained from environmental water samples, snail tissue samples, and positive controls collected from freshwater ecosystems in the Czech Republic and Slovakia. In addition to the raw paired-end FASTQ files, the repository includes sample metadata, sample identifiers, and the corresponding forward and reverse MID-barcoded primer combinations used for sample multiplexing during Illumina sequencing. The data were generated to assess avian schistosome diversity and evaluate the performance of multiple surveillance approaches for these medically important parasites responsible for cercarial dermatitis (swimmer's itch).