SeCAT (Sequence Consensus Amplicon Trimming): a simulation-informed Nextflow pipeline for cross-study harmonisation of 16S rRNA metabarcoding datasets

SeCAT harmonised 13 marine 16S rRNA metabarcoding studies by trimming to a shared consensus window, collapsing 20,891 primer-specific variants into 12,667 MetaASVs.

• Why it matters: Cross-study synthesis is limited because different primer pairs yield sequences that may not be positionally comparable, and existing batch-correction or taxonomic aggregation does not verify positional alignment before merging.
• What they did: The Nextflow pipeline maps each study’s variants onto a full-length 16S reference alignment, finds the largest shared window, and uses simulations to test whether trimming degrades community structure across 72 study–rank combinations.
• The result: Twelve studies passed or were cautioned (31 passes, 38 cautions, three failures), and 11 harmonised datasets (682 samples) preserved family-level structure (Mantel r = 1.00; Procrustes m² < 0.001) while recovering alpha diversity (intraclass correlations 0.93–1.00).

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