More and more, large projects manage to squeeze in one extra run after an assembly has started. It would save run time to add the reads to an assembly, even if it meant some sacrifice to overall assembly quality. (Submit on behalf of an external user.)
Option 1) Create a module to add one more run to an overlap store. For instance, an incremental addition might get trimmed relative to existing overlaps while existing reads don't get trimmed relative to new reads. The pipeline would then start at unitigs.
Option 2) Allow mated reads to enter the scaffold module. They might assist scaffolding and possibly consensus. Since they are untrimmed, they might be used only if they map full length.
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