Tourmaline and QIIME 2 files for 12S (fish) and 16S (microbes) amplicon metabarcoding associated with Sterivex eDNA methods development in Biscayne Bay, Florida (https://github.com/aomlomics/sterivex). Files are associated with sequence processing using either stand-alone QIIME 2 (12S folder) or Tourmaline (16S folder), which is a recently developed program that wraps QIIME 2 and Snakemake. Taxonomy was assigned to sequences using QIIME 2-formatted reference database for 16S (SILVA; v.138.1), 16S chloroplasts (PR2; v.4.12), and 12S (Mitohelper; March 2021 release). Folders with intermediate and final output files: 16S folder - file outputs from Tourmaline 16S chloroplast folder - files from QIIME 2 12S folder - files from QIIME 2 Reference database artifact files (.qza) used to assign taxonomy: silva-138-99-tax.qza silva-138-99-seqs.qza pr2_plastid_seqs.qza pr2_plastid_tax.qza 12S-16S-18S-seqs_March2021.qza 12S-16S-18S-tax_March2021.qza These files are associated with the following project: https://github.com/aomlomics/sterivex. Raw FASTQ sequence data are available in NCBI SRA under BioProject ID PRJNA728349.