Processed data and custom SILVA138 database for 18S metabarcoding analysis of non-overlapping paired-end reads

This dataset contains processed data, metadata, QIIME 2 artifacts, taxonomic assignment tables, control-sample outputs, non-inoculated sample audit tables, and a custom SILVA138 database used in the manuscript “Non-overlapping paired-end reads in 18S metabarcoding: concatenation of prefiltered reads enables fecal eukaryome profiling”. The dataset supports an 18S rRNA V4-V5 metabarcoding workflow developed for Illumina NovaSeq paired-end reads generated with a 500-cycle configuration (250 × 250 bp). The workflow evaluates pre-trimming strategies, read-processing approaches for non-overlapping paired-end reads, ASV inference with DADA2, and taxonomic assignment using PR2, SILVA132, and a custom SILVA138 database. Raw paired-end FASTQ files are not included in this Zenodo record and will be deposited separately in the NCBI Sequence Read Archive.