MarkerFlow: a generalised, marker-agnostic metabarcoding pipeline

MarkerFlow is a reproducible Illumina paired-end amplicon metabarcoding pipeline (merge, quality check, primer trimming, DADA2 ASV inference, and taxonomy assignment) that is configurable for any marker, with ready-to-use configurations for 18S (protists), ITS (fungi), and 16S (bacteria/archaea). It also includes a downstream statistics stage (filtering, rarefaction, and dataset-quality diagnostics).