Refers to a data processing pipeline that takes the raw sequence data from high-throughput sequencing (often 20 million sequences or more) and transforms it into usable ecological data. Key steps for metabarcoding pipelines include quality filtering, trimming, merging paired ends, removal of sequencing errors such as chimeras, clustering of similar sequences into molecular taxonomic units (each of which approximately represents a species), and matching one sequence from each cluster against a reference database. The output is a species-by-sample table showing how many sequences from each sample were identified as each species.

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