European marine plankton time-series ASV tables (SSU V4V5, 18S V4, 16S V3V4)

This dataset provides Amplicon Sequence Variant (ASV) tables derived from DNA metabarcoding of marine plankton samples collected across 10 European time-series. It aims to support comparative analyses of marine biodiversity dynamics over recent decades. More information about time-series here. Raw metabarcoding data were processed using the nf-core/ampliseq workflow (v2.13.0) with DADA2 for ASV inference. Taxonomic assignment was performed against PR2 v5.1.0 and SILVA v138.2. The dataset includes ASV tables for three genetic markers (SSU V4V5, 18S V4, and 16S V3V4), each organized in multiple files per marker: A README (HTML) detailing file contents and parameters (b5d-time-series_{marker}_README.html), ASV read counts in time-series samples (b5d-time-series_{marker}_dada2_counts.tsv.gz), ASV descriptions (taxonomy, total abundance/occurrence: b5d-time-series_{marker}_dada2_asvs.tsv.gz), ASV sequences in FASTA format (b5d-time-series_{marker}_dada2_asvs.fasta.gz), Alternative taxonomic assignments (b5d-time-series_{marker}_dada2_taxo_extra.tsv.gz), Code archive with scripts launching the Nextflow workflow and formatting outputs (b5d-time-series_{marker}_ampliseq-1.1.0.zip), nf-core/ampliseq reports detailing each bioinformatic step (b5d-time-series_{marker}_ampliseq_reports.zip), Read counts per bioinformatic step (b5d-time-series_{marker}_dada2_overall_summary.tsv.gz). Samples metadata (b5d-time-series_metadata.tsv.gz) covers ENA/NCBI accession numbers (run, sample, study), sample names, PCR primers, depths, size fractions, dates, sample types, genetic markers, and geographic coordinates. Negative controls were included and flagged. This work was supported by BIOcean5D.