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Consensus sequence pileup/masking methods. Two amplicons are shown with fragments (either illumina read pairs, or unpaired nanopore reads) mapped to the consensus. The fragments from amplicon 1 contribute to pileup at B-E, and do not count towards the primer regions A-B or E-F. Similarly, the fragments from amplicon 2 contribute to coverage at D-G (but not to C-D or G-H).
