General question about make.contigs

General question about make.contigs: What happens with paired reads that don’t overlap? In other words, if amplicon is longer than sum of paired reads, what will make.contigs do with those sequences?

They will get assembled so that they overlap by a single base or the two reads will get assembled so that they full overlap. You can then remove such sequences by not allowing contigs over a certain length or those that contain ambiguous base calls.

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